gene p beta se cmafTotal cmafUsed nsnpsTotal nsnpsUsed nmiss chr start end REF ALT TYPE refGene::location refGene::type ensGene::location Gene.Names Consequence.Embl refGene::location Gene.Embl FILTER MAF.lt:0 MAF.lt:0.001 MAF.lt:0.005 MAF.lt:0.01 MAF.lt:0.025 gerp.scores MAF ensGene::type Protein_position.Embl Amino_acids.Embl TCGA-AB-2878-03A-01W-0732-08.AD TCGA-AB-2917-03A-01W-0732-08.AD GENO.AML GENO.Control GENO.AML.filt GENO.Control.filt full.qual bad.coding maf.filter rare.in.group no.genotypes in.common.hit.gene hw.controls.ok on.x.y unannotated.hits not.flat.genotype are.repeats are.in.repeats ok.missing ok.missing.filt is.unwound.geno V16 hw.p.control.filt rare.in.group.filt no.genotypes.filt rare.in.controls.filt muts.in.cases quality.cases muts.in.controls quality.controls chr11:22646387:22646387:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 22646387 22646387 T C snp nonsynonymous SNV FANCF:NM_022725:exon1:c.A970G:p.K324E, nonsynonymous SNV FANCF missense_variant nonsynonymous SNV ENSG00000183161 PASS FALSE TRUE TRUE TRUE TRUE 2.29 0.000784929 ENSG00000183161:ENST00000327470:exon1:c.A970G:p.K324E, 324 K/E 21,0 21,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0161 99 chr11:22646421:22646421:T:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 22646421 22646421 T A snp nonsynonymous SNV FANCF:NM_022725:exon1:c.A936T:p.Q312H, nonsynonymous SNV FANCF missense_variant nonsynonymous SNV ENSG00000183161 PASS FALSE TRUE TRUE TRUE TRUE -3.9 0.000784929 ENSG00000183161:ENST00000327470:exon1:c.A936T:p.Q312H, 312 Q/H 21,0 21,0 0,0,146 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0129 99 chr11:22646724:22646724:C:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 22646724 22646724 C A snp nonsynonymous SNV FANCF:NM_022725:exon1:c.G633T:p.Q211H, nonsynonymous SNV FANCF missense_variant nonsynonymous SNV ENSG00000183161 PASS FALSE TRUE TRUE TRUE TRUE 1.6 0.000789889 ENSG00000183161:ENST00000327470:exon1:c.G633T:p.Q211H, 211 Q/H 21,0 21,0 0,0,145 0,1,487 0,0,145 0,1,465 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0047 99 chr11:22646800:22646800:G:A:snp 0.435974846195726 -0.0997409326424864 0.128035782343122 0.00704225352112676 0.00704225352112676 1 1 0 chr11 22646800 22646800 G A snp nonsynonymous SNV FANCF:NM_022725:exon1:c.C557T:p.A186V, nonsynonymous SNV FANCF missense_variant nonsynonymous SNV ENSG00000183161 PASS FALSE FALSE FALSE TRUE TRUE 1.82 0.00728155 ENSG00000183161:ENST00000327470:exon1:c.C557T:p.A186V, 186 A/V 21,0 21,0 0,1,144 1,6,466 0,1,144 0,4,413 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2959-03A-01W-0733-08 99 AOGC-02-0032,AOGC-02-0154,AOGC-02-0327,AOGC-02-0400,AOGC-03-0009,AOGC-08-0125,AOGC-08-0311 64,99,25,6,99,99,99 chr11:65630637:65630637:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 65630637 65630637 G A snp nonsynonymous SNV MUS81:NM_025128:exon7:c.G707A:p.G236E, nonsynonymous SNV MUS81 missense_variant nonsynonymous SNV ENSG00000172732 PASS FALSE TRUE TRUE TRUE TRUE 3.74 0.000807754 ENSG00000172732:ENST00000308110:exon7:c.G707A:p.G236E,ENSG00000172732:ENST00000533035:exon7:c.G482A:p.G161E, 161 G/E 10,0 12,0 0,0,144 0,1,474 0,0,140 0,1,440 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0161 99 chr11:65630699:65630699:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 65630699 65630699 G A snp intronic MUS81 intronic MUS81 intron_variant intronic ENSG00000172732 PASS FALSE TRUE TRUE TRUE TRUE 4.29 0.000840336 ENSG00000172732 - - 2,0 3,0 0,0,140 0,1,454 0,0,130 0,1,409 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-05-0016 99 chr11:65631368:65631368:A:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 65631368 65631368 A C snp nonsynonymous SNV MUS81:NM_025128:exon10:c.A1055C:p.Q352P, nonsynonymous SNV MUS81 missense_variant nonsynonymous SNV ENSG00000172732 PASS FALSE TRUE TRUE TRUE TRUE 3.49 0.000792393 ENSG00000172732:ENST00000308110:exon10:c.A1055C:p.Q352P,ENSG00000172732:ENST00000533035:exon10:c.A830C:p.Q277P, 277 Q/P 33,0 26,0 0,0,145 0,1,485 0,0,145 0,1,456 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0229 99 chr11:65631972:65631972:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 65631972 65631972 G A snp nonsynonymous SNV MUS81:NM_025128:exon11:c.G1064A:p.R355Q, nonsynonymous SNV MUS81 missense_variant nonsynonymous SNV ENSG00000172732 PASS FALSE TRUE TRUE TRUE TRUE 4.98 0.000788644 ENSG00000172732:ENST00000308110:exon11:c.G1064A:p.R355Q,ENSG00000172732:ENST00000533035:exon11:c.G839A:p.R280Q, 280 R/Q 23,0 20,0 0,0,145 0,1,488 0,0,144 0,1,474 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0033 99 chr11:65632010:65632010:G:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 65632010 65632010 G T snp nonsynonymous SNV MUS81:NM_025128:exon11:c.G1102T:p.V368L, nonsynonymous SNV MUS81 missense_variant nonsynonymous SNV ENSG00000172732 PASS FALSE TRUE TRUE TRUE TRUE 5.91 0.000786164 ENSG00000172732:ENST00000308110:exon11:c.G1102T:p.V368L,ENSG00000172732:ENST00000533035:exon11:c.G877T:p.V293L, 293 V/L 32,0 20,0 0,0,145 0,1,490 0,0,145 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0252 99 chr11:65632251:65632251:G:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 65632251 65632251 G A snp nonsynonymous SNV MUS81:NM_025128:exon12:c.G1237A:p.A413T, nonsynonymous SNV MUS81 missense_variant nonsynonymous SNV ENSG00000172732 PASS FALSE FALSE TRUE TRUE TRUE 4.04 0.0015748 ENSG00000172732:ENST00000308110:exon12:c.G1237A:p.A413T,ENSG00000172732:ENST00000533035:exon12:c.G1012A:p.A338T, 338 A/T 21,0 34,0 0,0,145 0,2,488 0,0,143 0,2,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0114,AOGC-08-0316 99,99 chr11:65632817:65632817:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 65632817 65632817 G C snp intronic MUS81 intronic MUS81 non_coding_exon_variant,nc_transcript_variant intronic ENSG00000172732 PASS FALSE TRUE TRUE TRUE TRUE 2.71 0.00085034 ENSG00000172732 - - 9,0 4,0 0,0,143 0,1,444 0,0,130 0,1,403 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0439 99 chr11:67161056:67161056:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 67161056 67161056 G A snp synonymous SNV RAD9A:NM_001243224:exon1:c.G96A:p.L32L,RAD9A:NM_004584:exon4:c.G324A:p.L108L, synonymous SNV RAD9A 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000172613 PASS FALSE FALSE TRUE TRUE TRUE 3.09 0.0008 ENSG00000172613:ENST00000544620:exon4:c.G282A:p.L94L,ENSG00000172613:ENST00000542139:exon4:c.G324A:p.L108L,ENSG00000172613:ENST00000307980:exon4:c.G324A:p.L108L, - - 20,0 26,0 0,1,144 0,0,480 0,1,142 0,0,445 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2812-03B-01W-0728-08 99 chr11:67163497:67163497:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 67163497 67163497 G A snp splicing RAD9A(NM_004584:exon7:c.669+5G>A,NM_001243224:exon4:c.441+5G>A) splicing RAD9A splice_region_variant,intron_variant splicing ENSG00000172613 PASS FALSE TRUE TRUE TRUE TRUE 4.88 0.000821018 ENSG00000172613(ENST00000307980:exon7:c.669+5G>A,ENST00000538013:exon4:c.388+5G>A,ENST00000544620:exon7:c.627+5G>A) - - 27,0 15,0 0,0,145 0,1,463 0,0,145 0,1,422 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0025 99 chr11:67164704:67164704:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 67164704 67164704 C T snp synonymous SNV RAD9A:NM_001243224:exon7:c.C699T:p.A233A,RAD9A:NM_004584:exon10:c.C927T:p.A309A, synonymous SNV RAD9A 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000172613 PASS FALSE TRUE TRUE TRUE TRUE 4.28 0.000789889 ENSG00000172613:ENST00000307980:exon10:c.C927T:p.A309A, - - 21,0 9,0 0,0,142 0,1,490 0,0,135 0,1,455 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0025 99 chr11:94178933:94178933:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94178933 94178933 T C snp intronic MRE11A intronic MRE11A non_coding_exon_variant,nc_transcript_variant intronic ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 3.59 0.000786164 ENSG00000020922 - - 20,0 15,0 0,0,145 0,1,490 0,0,144 0,1,477 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0041 91 chr11:94179032:94179032:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94179032 94179032 C T snp nonsynonymous SNV MRE11A:NM_005591:exon16:c.G1811A:p.R604H, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 0.487 0.000786164 ENSG00000020922:ENST00000407439:exon16:c.G1820A:p.R607H,ENSG00000020922:ENST00000393241:exon16:c.G1808A:p.R603H,ENSG00000020922:ENST00000323929:exon16:c.G1811A:p.R604H, 604 R/H 20,0 20,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0267 99 chr11:94179045:94179045:C:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94179045 94179045 C G snp nonsynonymous SNV MRE11A:NM_005591:exon16:c.G1798C:p.E600Q, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE FALSE TRUE TRUE TRUE 3.67 0.000786164 ENSG00000020922:ENST00000407439:exon16:c.G1807C:p.E603Q,ENSG00000020922:ENST00000393241:exon16:c.G1795C:p.E599Q,ENSG00000020922:ENST00000323929:exon16:c.G1798C:p.E600Q, 600 E/Q 20,0 20,0 0,1,144 0,0,491 0,1,144 0,0,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2810-03B-01W-0728-08 99 chr11:94180454:94180454:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94180454 94180454 G A snp stopgain SNV MRE11A:NM_005591:exon15:c.C1714T:p.R572X,MRE11A:NM_005590:exon15:c.C1714T:p.R572X, stopgain SNV MRE11A stop_gained stopgain SNV ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 5.17 0.000786164 ENSG00000020922:ENST00000407439:exon15:c.C1723T:p.R575X,ENSG00000020922:ENST00000323977:exon15:c.C1714T:p.R572X,ENSG00000020922:ENST00000393241:exon15:c.C1714T:p.R572X,ENSG00000020922:ENST00000323929:exon15:c.C1714T:p.R572X, 572 R/* 20,0 21,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0150 99 chr11:94180501:94180501:T:C:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 94180501 94180501 T C snp nonsynonymous SNV MRE11A:NM_005591:exon15:c.A1667G:p.N556S,MRE11A:NM_005590:exon15:c.A1667G:p.N556S, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE FALSE TRUE TRUE TRUE 3.24 0.00156986 ENSG00000020922:ENST00000407439:exon15:c.A1676G:p.N559S,ENSG00000020922:ENST00000323977:exon15:c.A1667G:p.N556S,ENSG00000020922:ENST00000393241:exon15:c.A1667G:p.N556S,ENSG00000020922:ENST00000323929:exon15:c.A1667G:p.N556S, 556 N/S 20,0 21,0 0,0,146 0,2,489 0,0,145 0,2,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0210,AOGC-14-0059 99,99 chr11:94189501:94189501:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94189501 94189501 G A snp nonsynonymous SNV MRE11A:NM_005591:exon14:c.C1504T:p.R502C,MRE11A:NM_005590:exon14:c.C1504T:p.R502C, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 5.78 0.000787402 ENSG00000020922:ENST00000407439:exon14:c.C1513T:p.R505C,ENSG00000020922:ENST00000323977:exon14:c.C1504T:p.R502C,ENSG00000020922:ENST00000393241:exon14:c.C1504T:p.R502C,ENSG00000020922:ENST00000323929:exon14:c.C1504T:p.R502C, 502 R/C 20,0 23,0 0,0,145 0,1,489 0,0,145 0,1,477 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0393 99 chr11:94192594:94192594:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94192594 94192594 C T snp nonsynonymous SNV MRE11A:NM_005591:exon13:c.G1480A:p.E494K,MRE11A:NM_005590:exon13:c.G1480A:p.E494K, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 5.89 0.000787402 ENSG00000020922:ENST00000407439:exon13:c.G1489A:p.E497K,ENSG00000020922:ENST00000323977:exon13:c.G1480A:p.E494K,ENSG00000020922:ENST00000393241:exon13:c.G1480A:p.E494K,ENSG00000020922:ENST00000323929:exon13:c.G1480A:p.E494K, 494 E/K 22,0 20,0 0,1,145 0,0,489 0,1,145 0,0,476 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2883-03A-01W-0732-08 99 chr11:94192599:94192599:G:T:snp 0.0262088112929376 0.273524720893143 0.123037322324538 0.00938967136150235 0.00938967136150235 1 1 0 chr11 94192599 94192599 G T snp nonsynonymous SNV MRE11A:NM_005591:exon13:c.C1475A:p.A492D,MRE11A:NM_005590:exon13:c.C1475A:p.A492D, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE FALSE FALSE TRUE TRUE 4.97 0.00944882 ENSG00000020922:ENST00000407439:exon13:c.C1484A:p.A495D,ENSG00000020922:ENST00000323977:exon13:c.C1475A:p.A492D,ENSG00000020922:ENST00000393241:exon13:c.C1475A:p.A492D,ENSG00000020922:ENST00000323929:exon13:c.C1475A:p.A492D, 492 A/D 22,0 20,0 0,6,140 0,6,483 0,6,140 0,6,472 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2804-03B-01W-0728-08,TCGA-AB-2838-03A-01W-0726-08,TCGA-AB-2842-03A-01W-0726-08,TCGA-AB-2867-03B-01W-0728-08,TCGA-AB-2916-03A-01W-0732-08,TCGA-AB-2935-03A-01W-0745-08 99,99,99,99,99,99 AOGC-02-0081,AOGC-02-0165,AOGC-02-0400,AOGC-02-0524,AOGC-03-0084,AOGC-14-0326 99,99,99,99,99,99 chr11:94192654:94192654:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94192654 94192654 C T snp nonsynonymous SNV MRE11A:NM_005591:exon13:c.G1420A:p.V474M,MRE11A:NM_005590:exon13:c.G1420A:p.V474M, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 5.8 0.000784929 ENSG00000020922:ENST00000407439:exon13:c.G1429A:p.V477M,ENSG00000020922:ENST00000323977:exon13:c.G1420A:p.V474M,ENSG00000020922:ENST00000393241:exon13:c.G1420A:p.V474M,ENSG00000020922:ENST00000323929:exon13:c.G1420A:p.V474M, 474 V/M 22,0 20,0 0,0,146 0,1,490 0,0,146 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0252 99 chr11:94201047:94201047:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94201047 94201047 G A snp nonsynonymous SNV MRE11A:NM_005591:exon10:c.C1030T:p.L344F,MRE11A:NM_005590:exon10:c.C1030T:p.L344F, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 6.06 0.000786164 ENSG00000020922:ENST00000407439:exon10:c.C1039T:p.L347F,ENSG00000020922:ENST00000323977:exon10:c.C1030T:p.L344F,ENSG00000020922:ENST00000393241:exon10:c.C1030T:p.L344F,ENSG00000020922:ENST00000323929:exon10:c.C1030T:p.L344F, 344 L/F 25,0 22,0 0,0,145 0,1,490 0,0,145 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0087 99 chr11:94212851:94212851:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94212851 94212851 C T snp nonsynonymous SNV MRE11A:NM_005591:exon5:c.G391A:p.D131N,MRE11A:NM_005590:exon5:c.G391A:p.D131N, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 5.64 0.000784929 ENSG00000020922:ENST00000540013:exon5:c.G391A:p.D131N,ENSG00000020922:ENST00000407439:exon5:c.G400A:p.D134N,ENSG00000020922:ENST00000323977:exon5:c.G391A:p.D131N,ENSG00000020922:ENST00000393241:exon5:c.G391A:p.D131N,ENSG00000020922:ENST00000323929:exon5:c.G391A:p.D131N, 131 D/N 20,0 21,0 0,0,146 0,1,490 0,0,145 0,1,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0210 99 chr11:94212884:94212884:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 94212884 94212884 T C snp nonsynonymous SNV MRE11A:NM_005591:exon5:c.A358G:p.I120V,MRE11A:NM_005590:exon5:c.A358G:p.I120V, nonsynonymous SNV MRE11A missense_variant nonsynonymous SNV ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 4.24 0.000784929 ENSG00000020922:ENST00000540013:exon5:c.A358G:p.I120V,ENSG00000020922:ENST00000407439:exon5:c.A367G:p.I123V,ENSG00000020922:ENST00000323977:exon5:c.A358G:p.I120V,ENSG00000020922:ENST00000536754:exon5:c.A358G:p.I120V,ENSG00000020922:ENST00000393241:exon5:c.A358G:p.I120V,ENSG00000020922:ENST00000323929:exon5:c.A358G:p.I120V, 120 I/V 20,0 21,0 0,0,146 0,1,490 0,0,145 0,1,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0152 99 chr11:94225876:94225876:T:C:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr11 94225876 94225876 T C snp intronic MRE11A UTR5 MRE11A 5_prime_UTR_variant intronic ENSG00000020922 PASS FALSE FALSE TRUE TRUE TRUE 3.26 0.00236967 ENSG00000020922 - - 21,0 7,0 0,0,145 0,3,485 0,0,144 0,1,399 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0504,AOGC-08-0004,AOGC-08-0303 58,99,99 chr11:108106399:108106399:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108106399 108106399 G A snp nonsynonymous SNV ATM:NM_000051:exon5:c.G334A:p.A112T, nonsynonymous SNV ATM missense_variant,splice_region_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 4.71 0.000791139 ENSG00000149311:ENST00000527805:exon5:c.G334A:p.A112T,ENSG00000149311:ENST00000452508:exon6:c.G334A:p.A112T,ENSG00000149311:ENST00000278616:exon5:c.G334A:p.A112T,ENSG00000149311:ENST00000601453:exon6:c.G334A:p.A112T, 112 A/T 31,0 8,0 0,1,145 0,0,486 0,1,144 0,0,436 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2900-03A-01W-0733-08 99 chr11:108114774:108114774:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108114774 108114774 A T snp synonymous SNV ATM:NM_000051:exon6:c.A591T:p.G197G, synonymous SNV ATM synonymous_variant synonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 4.44 0.000789889 ENSG00000149311:ENST00000527805:exon6:c.A591T:p.G197G,ENSG00000149311:ENST00000452508:exon7:c.A591T:p.G197G,ENSG00000149311:ENST00000527891:exon5:c.A426T:p.G142G,ENSG00000149311:ENST00000278616:exon6:c.A591T:p.G197G, 197 G 20,0 7,0 0,0,145 0,1,487 0,0,144 0,1,442 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0152 99 chr11:108114792:108114792:C:T:snp 0.461090014386246 -0.139359698681732 0.189076858826633 0.00234741784037559 0.00234741784037559 1 1 0 chr11 108114792 108114792 C T snp synonymous SNV ATM:NM_000051:exon6:c.C609T:p.D203D, synonymous SNV ATM synonymous_variant synonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 4.4 0.00236967 ENSG00000149311:ENST00000527805:exon6:c.C609T:p.D203D,ENSG00000149311:ENST00000452508:exon7:c.C609T:p.D203D,ENSG00000149311:ENST00000527891:exon5:c.C444T:p.D148D,ENSG00000149311:ENST00000278616:exon6:c.C609T:p.D203D, 203 D 20,0 20,0 0,0,145 1,1,486 0,0,145 1,0,426 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 0.00117233294255569 1 0 1 AOGC-03-0041,AOGC-08-0125 82,12 chr11:108115523:108115523:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108115523 108115523 A G snp nonsynonymous SNV ATM:NM_000051:exon7:c.A671G:p.K224R, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 5.36 0.000784929 ENSG00000149311:ENST00000527805:exon7:c.A671G:p.K224R,ENSG00000149311:ENST00000452508:exon8:c.A671G:p.K224R,ENSG00000149311:ENST00000278616:exon7:c.A671G:p.K224R, 224 K/R 23,0 23,0 0,0,146 0,1,490 0,0,145 0,1,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0302 99 chr11:108117787:108117787:C:T:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 108117787 108117787 C T snp nonsynonymous SNV ATM:NM_000051:exon8:c.C998T:p.S333F, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 3.85 0.00157978 ENSG00000149311:ENST00000527805:exon8:c.C998T:p.S333F,ENSG00000149311:ENST00000452508:exon9:c.C998T:p.S333F,ENSG00000149311:ENST00000278616:exon8:c.C998T:p.S333F, 333 S/F 20,0 17,14 0,1,144 0,1,487 0,1,144 0,1,429 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2917-03A-01W-0732-08 99 AOGC-05-0013 99 chr11:108119654:108119654:T:G:snp 0.202168134675384 0.270078740157481 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr11 108119654 108119654 T G snp intronic ATM intronic ATM splice_region_variant,intron_variant intronic ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 3.62 0.00318979 ENSG00000149311 - - 21,0 8,0 0,2,143 0,2,480 0,2,139 0,2,437 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2830-03B-01W-0728-08,TCGA-AB-2895-03A-01W-0733-08 99,99 AOGC-01-0003,AOGC-02-0137 99,12 chr11:108119823:108119823:T:C:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 108119823 108119823 T C snp nonsynonymous SNV ATM:NM_000051:exon9:c.T1229C:p.V410A, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 5.07 0.00159236 ENSG00000149311:ENST00000527805:exon9:c.T1229C:p.V410A,ENSG00000149311:ENST00000452508:exon10:c.T1229C:p.V410A,ENSG00000149311:ENST00000278616:exon9:c.T1229C:p.V410A, 410 V/A 21,0 20,0 0,0,145 0,2,481 0,0,145 0,2,402 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0088,AOGC-02-0496 99,88 chr11:108121495:108121495:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108121495 108121495 T C snp synonymous SNV ATM:NM_000051:exon10:c.T1303C:p.L435L, synonymous SNV ATM synonymous_variant synonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 4.76 0.000786164 ENSG00000149311:ENST00000527805:exon10:c.T1303C:p.L435L,ENSG00000149311:ENST00000452508:exon11:c.T1303C:p.L435L,ENSG00000149311:ENST00000278616:exon10:c.T1303C:p.L435L, 435 L 33,0 25,0 0,0,145 0,1,490 0,0,145 0,1,489 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0152 99 chr11:108122604:108122604:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108122604 108122604 A G snp nonsynonymous SNV ATM:NM_000051:exon11:c.A1648G:p.I550V, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE -4.75 0.000788644 ENSG00000149311:ENST00000527805:exon11:c.A1648G:p.I550V,ENSG00000149311:ENST00000452508:exon12:c.A1648G:p.I550V,ENSG00000149311:ENST00000278616:exon11:c.A1648G:p.I550V, 550 I/V 21,0 21,0 0,0,146 0,1,487 0,0,146 0,1,469 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0152 99 chr11:108122700:108122700:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108122700 108122700 T C snp nonsynonymous SNV ATM:NM_000051:exon11:c.T1744C:p.F582L, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 1.13 0.000793651 ENSG00000149311:ENST00000527805:exon11:c.T1744C:p.F582L,ENSG00000149311:ENST00000452508:exon12:c.T1744C:p.F582L,ENSG00000149311:ENST00000278616:exon11:c.T1744C:p.F582L, 582 F/L 21,0 21,0 0,1,145 0,0,484 0,1,144 0,0,442 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2930-03A-01W-0761-09 99 chr11:108126934:108126934:A:T:snp 1.1370993779307e-09 0.781847133757963 0.128405935709664 0.00860719874804382 0.00860719874804382 1 1 0 chr11 108126934 108126934 A T snp intronic ATM intronic ATM splice_region_variant,intron_variant intronic ENSG00000149311 PASS TRUE TRUE TRUE TRUE TRUE -3.12 0.00866142 ENSG00000149311 - - 25,0 11,0 0,11,134 0,0,490 0,11,134 0,0,484 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2805-03B-01W-0728-08,TCGA-AB-2823-03B-01W-0728-08,TCGA-AB-2847-03B-01W-0728-08,TCGA-AB-2849-03B-01W-0728-08,TCGA-AB-2854-03B-01W-0728-08,TCGA-AB-2857-03B-01W-0728-08,TCGA-AB-2860-03B-01W-0728-08,TCGA-AB-2868-03B-01W-0728-08,TCGA-AB-2874-03A-01W-0732-08,TCGA-AB-2904-03A-01W-0732-08,TCGA-AB-2952-03A-01W-0733-08 50,53,48,22,73,90,50,87,17,30,41 chr11:108127089:108127089:A:C:snp 0.693155862310845 -0.0506658946149384 0.128405935709664 0.00860719874804382 0.00860719874804382 1 1 0 chr11 108127089 108127089 A C snp intronic ATM intronic ATM intron_variant intronic ENSG00000149311 PASS FALSE FALSE FALSE TRUE TRUE 2.9 0.0086478 ENSG00000149311 - - 28,0 20,0 0,2,143 0,9,482 0,2,143 0,9,471 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2823-03B-01W-0728-08,TCGA-AB-2865-03B-01W-0728-08 99,99 AOGC-02-0041,AOGC-02-0070,AOGC-02-0134,AOGC-03-0094,AOGC-05-0020,AOGC-08-0039,AOGC-08-0091,AOGC-08-0231,AOGC-14-0156 99,99,99,99,99,99,99,99,99 chr11:108139302:108139302:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108139302 108139302 C T snp nonsynonymous SNV ATM:NM_000051:exon18:c.C2804T:p.T935M, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE -1.33 0.000784929 ENSG00000149311:ENST00000527805:exon18:c.C2804T:p.T935M,ENSG00000149311:ENST00000452508:exon19:c.C2804T:p.T935M,ENSG00000149311:ENST00000278616:exon18:c.C2804T:p.T935M, 935 T/M 28,0 31,0 0,0,146 0,1,490 0,0,145 0,1,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0052 99 chr11:108141983:108141983:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108141983 108141983 T C snp nonsynonymous SNV ATM:NM_000051:exon20:c.T2927C:p.V976A, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 5.5 0.000786164 ENSG00000149311:ENST00000527805:exon20:c.T2927C:p.V976A,ENSG00000149311:ENST00000452508:exon21:c.T2927C:p.V976A,ENSG00000149311:ENST00000278616:exon20:c.T2927C:p.V976A, 976 V/A 26,0 27,0 0,1,144 0,0,491 0,1,144 0,0,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2871-03A-01W-0732-08 99 chr11:108150287:108150287:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108150287 108150287 A G snp synonymous SNV ATM:NM_000051:exon23:c.A3354G:p.T1118T, synonymous SNV ATM synonymous_variant synonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 2.01 0.000784929 ENSG00000149311:ENST00000527805:exon23:c.A3354G:p.T1118T,ENSG00000149311:ENST00000452508:exon24:c.A3354G:p.T1118T,ENSG00000149311:ENST00000278616:exon23:c.A3354G:p.T1118T, 1118 T 23,0 22,0 0,0,146 0,1,490 0,0,145 0,1,488 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0354 99 chr11:108150374:108150374:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108150374 108150374 T C snp intronic ATM intronic ATM intron_variant intronic ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 3.24 0.000789889 ENSG00000149311 - - 23,0 22,0 0,0,146 0,1,486 0,0,145 0,1,437 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0316 99 chr11:108163382:108163382:C:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 108163382 108163382 C T snp synonymous SNV ATM:NM_000051:exon30:c.C4473T:p.F1491F, synonymous SNV ATM non_coding_exon_variant,nc_transcript_variant synonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 4.08 0.0015748 ENSG00000149311:ENST00000452508:exon31:c.C4473T:p.F1491F,ENSG00000149311:ENST00000278616:exon30:c.C4473T:p.F1491F, - - 21,0 32,0 0,0,145 0,2,488 0,0,145 0,1,459 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0354,AOGC-08-0106 69,54 chr11:108163462:108163462:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108163462 108163462 A G snp nonsynonymous SNV ATM:NM_000051:exon30:c.A4553G:p.H1518R, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 5.01 0.000784929 ENSG00000149311:ENST00000452508:exon31:c.A4553G:p.H1518R,ENSG00000149311:ENST00000278616:exon30:c.A4553G:p.H1518R, 1518 H/R 21,0 32,0 0,0,146 0,1,490 0,0,146 0,1,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0081 99 chr11:108163486:108163486:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108163486 108163486 C T snp nonsynonymous SNV ATM:NM_000051:exon30:c.C4577T:p.P1526L, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 5.01 0.000784929 ENSG00000149311:ENST00000452508:exon31:c.C4577T:p.P1526L,ENSG00000149311:ENST00000278616:exon30:c.C4577T:p.P1526L, 1526 P/L 21,0 32,0 0,0,146 0,1,490 0,0,146 0,1,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0305 99 chr11:108164137:108164137:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108164137 108164137 T C snp nonsynonymous SNV ATM:NM_000051:exon31:c.T4709C:p.V1570A, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 4.16 0.000787402 ENSG00000149311:ENST00000452508:exon32:c.T4709C:p.V1570A,ENSG00000149311:ENST00000278616:exon31:c.T4709C:p.V1570A, 1570 V/A 21,0 24,0 0,1,145 0,0,489 0,1,144 0,0,441 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2858-03D-01W-0755-09 99 chr11:108165656:108165656:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108165656 108165656 A G snp synonymous SNV ATM:NM_000051:exon32:c.A4779G:p.E1593E, nonsynonymous SNV ATM missense_variant,splice_region_variant synonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 4.52 0.000784929 ENSG00000149311:ENST00000531525:exon4:c.A446G:p.K149R, 149 K/R 20,0 21,0 0,0,146 0,1,490 0,0,145 0,1,462 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0106 99 chr11:108165727:108165727:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108165727 108165727 T C snp nonsynonymous SNV ATM:NM_000051:exon32:c.T4850C:p.L1617P, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 5.55 0.000786164 ENSG00000149311:ENST00000452508:exon33:c.T4850C:p.L1617P,ENSG00000149311:ENST00000278616:exon32:c.T4850C:p.L1617P, 1617 L/P 20,0 21,0 0,0,145 0,1,490 0,0,145 0,1,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-05-0008 99 chr11:108168084:108168084:C:T:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 108168084 108168084 C T snp synonymous SNV ATM:NM_000051:exon33:c.C4980T:p.N1660N, synonymous SNV ATM non_coding_exon_variant,nc_transcript_variant synonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 2.06 0.00157233 ENSG00000149311:ENST00000452508:exon34:c.C4980T:p.N1660N,ENSG00000149311:ENST00000278616:exon33:c.C4980T:p.N1660N, - - 21,0 22,0 0,1,144 0,1,490 0,1,144 0,0,447 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2940-03A-01W-0733-08 99 AOGC-02-0530 57 chr11:108170506:108170506:A:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108170506 108170506 A C snp nonsynonymous SNV ATM:NM_000051:exon34:c.A5071C:p.S1691R, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 2.65 0.000788644 ENSG00000149311:ENST00000452508:exon35:c.A5071C:p.S1691R,ENSG00000149311:ENST00000278616:exon34:c.A5071C:p.S1691R, 1691 S/R 24,0 21,0 0,0,145 0,1,488 0,0,145 0,1,455 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0049 99 chr11:108170524:108170524:A:G:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 108170524 108170524 A G snp nonsynonymous SNV ATM:NM_000051:exon34:c.A5089G:p.T1697A, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 1.7 0.0015748 ENSG00000149311:ENST00000452508:exon35:c.A5089G:p.T1697A,ENSG00000149311:ENST00000278616:exon34:c.A5089G:p.T1697A, 1697 T/A 24,0 21,0 0,1,145 0,1,488 0,1,144 0,1,458 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2908-03A-01W-0745-08 99 AOGC-03-0124 99 chr11:108173670:108173670:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108173670 108173670 A T snp nonsynonymous SNV ATM:NM_000051:exon36:c.A5410T:p.I1804F, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE -5.84 0.000787402 ENSG00000149311:ENST00000452508:exon37:c.A5410T:p.I1804F,ENSG00000149311:ENST00000278616:exon36:c.A5410T:p.I1804F, 1804 I/F 20,0 24,0 0,0,146 0,1,488 0,0,145 0,1,469 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0012 99 chr11:108175463:108175463:A:T:snp 0.733167316798394 0.0547016274864384 0.160455166401833 0.0054773082942097 0.0054773082942097 1 1 0 chr11 108175463 108175463 A T snp nonsynonymous SNV ATM:NM_000051:exon37:c.A5558T:p.D1853V, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE FALSE TRUE TRUE 5.52 0.00550314 ENSG00000149311:ENST00000452508:exon38:c.A5558T:p.D1853V,ENSG00000149311:ENST00000278616:exon37:c.A5558T:p.D1853V, 1853 D/V 21,0 20,0 0,2,143 0,5,486 0,2,143 0,5,478 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2884-03A-01W-0732-08,TCGA-AB-2918-03A-01W-0745-08 99,99 AOGC-02-0076,AOGC-02-0087,AOGC-02-0105,AOGC-02-0342,AOGC-08-0269 99,99,99,99,99 chr11:108178767:108178767:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108178767 108178767 T C snp intronic ATM intronic ATM non_coding_exon_variant,nc_transcript_variant intronic ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 5.41 0.000787402 ENSG00000149311 - - 13,0 8,0 0,0,145 0,1,489 0,0,145 0,1,481 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0466 99 chr11:108180945:108180945:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108180945 108180945 G C snp nonsynonymous SNV ATM:NM_000051:exon39:c.G5821C:p.V1941L, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 5.7 0.000786164 ENSG00000149311:ENST00000452508:exon40:c.G5821C:p.V1941L,ENSG00000149311:ENST00000278616:exon39:c.G5821C:p.V1941L, 1941 V/L 21,0 21,0 0,0,145 0,1,490 0,0,145 0,1,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0317 99 chr11:108186503:108186503:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108186503 108186503 A T snp intronic ATM intronic ATM intron_variant intronic ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 4.79 0.000787402 ENSG00000149311,ENSG00000166323 - - 11,0 2,0 0,0,144 0,1,490 0,0,120 0,1,487 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0116 99 chr11:108186610:108186610:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108186610 108186610 G A snp nonsynonymous SNV ATM:NM_000051:exon41:c.G6067A:p.G2023R, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 5.33 0.000786164 ENSG00000149311:ENST00000452508:exon42:c.G6067A:p.G2023R,ENSG00000149311:ENST00000278616:exon41:c.G6067A:p.G2023R, 2023 G/R 20,0 20,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0192 99 chr11:108196068:108196068:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108196068 108196068 T G snp nonsynonymous SNV ATM:NM_000051:exon46:c.T6604G:p.Y2202D, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 5.42 0.000783699 ENSG00000149311:ENST00000452508:exon47:c.T6604G:p.Y2202D,ENSG00000149311:ENST00000278616:exon46:c.T6604G:p.Y2202D, 2202 Y/D 34,0 21,0 0,0,147 0,1,490 0,0,145 0,1,479 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0166 99 chr11:108196259:108196259:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108196259 108196259 C T snp synonymous SNV ATM:NM_000051:exon46:c.C6795T:p.F2265F, synonymous SNV ATM non_coding_exon_variant,nc_transcript_variant synonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 3.54 0.000791139 ENSG00000149311:ENST00000452508:exon47:c.C6795T:p.F2265F,ENSG00000149311:ENST00000278616:exon46:c.C6795T:p.F2265F, - - 34,0 21,0 0,0,145 0,1,486 0,0,145 0,1,448 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0187 99 chr11:108198384:108198384:C:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108198384 108198384 C G snp nonsynonymous SNV ATM:NM_000051:exon48:c.C6988G:p.L2330V, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 2.69 0.000786164 ENSG00000149311:ENST00000452508:exon49:c.C6988G:p.L2330V,ENSG00000149311:ENST00000278616:exon48:c.C6988G:p.L2330V, 2330 L/V 27,0 22,0 0,1,144 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2901-03A-01W-0733-08 99 chr11:108200946:108200946:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108200946 108200946 C T snp nonsynonymous SNV ATM:NM_000051:exon50:c.C7313T:p.T2438I, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 3.79 0.000793651 ENSG00000149311:ENST00000452508:exon51:c.C7313T:p.T2438I,ENSG00000149311:ENST00000278616:exon50:c.C7313T:p.T2438I, 2438 T/I 23,0 7,0 0,1,145 0,0,484 0,1,144 0,0,453 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2900-03A-01W-0733-08 99 chr11:108201023:108201023:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108201023 108201023 T C snp nonsynonymous SNV ATM:NM_000051:exon50:c.T7390C:p.C2464R, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 4.7 0.000788644 ENSG00000149311:ENST00000452508:exon51:c.T7390C:p.C2464R,ENSG00000149311:ENST00000278616:exon50:c.T7390C:p.C2464R, 2464 C/R 23,0 22,0 0,0,146 0,1,487 0,0,145 0,1,472 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0180 99 chr11:108201127:108201127:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108201127 108201127 T C snp synonymous SNV ATM:NM_000051:exon50:c.T7494C:p.S2498S, synonymous SNV ATM non_coding_exon_variant,nc_transcript_variant synonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 2.22 0.000798722 ENSG00000149311:ENST00000452508:exon51:c.T7494C:p.S2498S,ENSG00000149311:ENST00000278616:exon50:c.T7494C:p.S2498S, - - 23,0 22,0 0,0,146 0,1,479 0,0,145 0,1,410 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-05-0013 59 chr11:108202177:108202177:G:A:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 108202177 108202177 G A snp nonsynonymous SNV ATM:NM_000051:exon51:c.G7522A:p.G2508R, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS TRUE TRUE TRUE TRUE TRUE 5.43 0.00157233 ENSG00000149311:ENST00000452508:exon52:c.G7522A:p.G2508R,ENSG00000149311:ENST00000278616:exon51:c.G7522A:p.G2508R, 2508 G/R 23,0 20,0 0,1,144 0,1,490 0,1,144 0,1,481 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2836-03B-01W-0728-08 99 AOGC-08-0237 16 chr11:108202772:108202772:G:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108202772 108202772 G T snp intronic ATM intronic ATM splice_region_variant,intron_variant intronic ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 1.3 0.000787402 ENSG00000149311,ENSG00000166323 - - 20,0 20,0 0,0,146 0,1,488 0,0,145 0,1,423 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0506 99 chr11:108203619:108203619:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108203619 108203619 C T snp nonsynonymous SNV ATM:NM_000051:exon53:c.C7919T:p.T2640I, nonsynonymous SNV ATM missense_variant nonsynonymous SNV ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 2.09 0.000791139 ENSG00000149311:ENST00000452508:exon54:c.C7919T:p.T2640I,ENSG00000149311:ENST00000278616:exon53:c.C7919T:p.T2640I, 2640 T/I 29,0 22,0 0,1,145 0,0,486 0,1,144 0,0,444 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2829-03B-01W-0728-08 99 chr11:108204604:108204604:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108204604 108204604 T C snp intronic ATM intronic ATM intron_variant intronic ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 4.31 0.000789889 ENSG00000149311,ENSG00000166323 - - 22,0 21,0 0,0,145 0,1,487 0,0,145 0,1,451 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0033 99 chr11:108216738:108216738:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108216738 108216738 G A snp intronic ATM intronic ATM intron_variant intronic ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 2.71 0.000797448 ENSG00000149311,ENSG00000166323 - - 11,0 2,0 0,0,143 0,1,483 0,0,138 0,1,412 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0206 99 chr11:108218013:108218013:C:T:snp 0.675730396862748 0.102201257861636 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr11 108218013 108218013 C T snp synonymous SNV ATM:NM_000051:exon59:c.C8592T:p.Y2864Y, synonymous SNV ATM non_coding_exon_variant,nc_transcript_variant synonymous SNV ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 2.49 0.00235479 ENSG00000149311:ENST00000452508:exon60:c.C8592T:p.Y2864Y,ENSG00000149311:ENST00000278616:exon59:c.C8592T:p.Y2864Y, - - 35,0 27,0 0,1,145 0,2,489 0,1,144 0,2,469 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2899-03A-01W-0733-08 99 AOGC-03-0172,AOGC-14-0141 99,99 chr11:108225659:108225659:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108225659 108225659 T C snp intronic ATM UTR3 ATM 3_prime_UTR_variant,NMD_transcript_variant intronic ENSG00000166323 PASS TRUE TRUE TRUE TRUE TRUE 3.54 0.000786164 ENSG00000166323 - - 42,0 19,0 0,1,144 0,0,491 0,1,144 0,0,482 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2864-03B-01W-0728-08 99 chr11:125499156:125499156:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 125499156 125499156 G A snp nonsynonymous SNV CHEK1:NM_001114121:exon4:c.G319A:p.A107T,CHEK1:NM_001274:exon4:c.G319A:p.A107T,CHEK1:NM_001244846:exon4:c.G319A:p.A107T,CHEK1:NM_001114122:exon4:c.G319A:p.A107T, nonsynonymous SNV CHEK1 missense_variant nonsynonymous SNV ENSG00000149554 PASS FALSE TRUE TRUE TRUE TRUE 5.32 0.000786164 ENSG00000149554:ENST00000526937:exon4:c.G319A:p.A107T,ENSG00000149554:ENST00000428830:exon4:c.G319A:p.A107T,ENSG00000149554:ENST00000278916:exon3:c.G319A:p.A107T,ENSG00000149554:ENST00000534685:exon5:c.G319A:p.A107T,ENSG00000149554:ENST00000525396:exon4:c.G319A:p.A107T,ENSG00000149554:ENST00000534070:exon4:c.G319A:p.A107T,ENSG00000149554:ENST00000532669:exon2:c.G82A:p.A28T,ENSG00000149554:ENST00000524737:exon3:c.G319A:p.A107T,ENSG00000149554:ENST00000438015:exon4:c.G319A:p.A107T,ENSG00000149554:ENST00000544373:exon4:c.G319A:p.A107T,ENSG00000149554:ENST00000527013:exon4:c.G319A:p.A107T,ENSG00000149554:ENST00000427383:exon3:c.G367A:p.A123T, 107 A/T 22,0 25,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0424 99 chr11:125499193:125499193:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 125499193 125499193 T G snp splicing CHEK1(NM_001114122:exon4:c.354+2T>G,NM_001114121:exon4:c.354+2T>G,NM_001244846:exon4:c.354+2T>G,NM_001274:exon4:c.354+2T>G) splicing CHEK1 splice_donor_variant splicing ENSG00000149554 PASS TRUE TRUE TRUE TRUE TRUE 4.91 0.000786164 ENSG00000149554(ENST00000438015:exon4:c.354+2T>G,ENST00000525396:exon4:c.354+2T>G,ENST00000427383:exon3:c.402+2T>G,ENST00000428830:exon4:c.354+2T>G,ENST00000544373:exon4:c.354+2T>G,ENST00000527013:exon4:c.354+2T>G,ENST00000526937:exon4:c.354+2T>G,ENST00000534685:exon5:c.354+2T>G,ENST00000534070:exon4:c.354+2T>G,ENST00000524737:exon3:c.354+2T>G,ENST00000278916:exon3:c.354+2T>G,ENST00000532669:exon2:c.117+2T>G) - - 22,0 25,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0366 99 chr11:125514323:125514323:A:G:snp 0.876614424938906 -0.017714285714285 0.114092537139377 0.0109546165884194 0.0109546165884194 1 1 0 chr11 125514323 125514323 A G snp intronic CHEK1 intronic CHEK1 intron_variant intronic ENSG00000149554 PASS FALSE FALSE FALSE TRUE TRUE 2.89 0.011041 ENSG00000149554 - - 24,0 7,0 0,3,142 0,11,478 0,3,141 0,11,465 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2825-03B-01W-0728-08,TCGA-AB-2941-03A-01W-0745-08,TCGA-AB-2949-03A-01W-0733-08 99,99,99 AOGC-02-0044,AOGC-02-0050,AOGC-02-0188,AOGC-02-0535,AOGC-03-0062,AOGC-03-0066,AOGC-03-0091,AOGC-03-0167,AOGC-08-0069,AOGC-08-0244,AOGC-08-0279 99,99,99,59,99,79,99,99,99,99,63 chr11:125514330:125514330:A:T:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr11 125514330 125514330 A T snp intronic CHEK1 intronic CHEK1 intron_variant intronic ENSG00000149554 PASS FALSE FALSE TRUE TRUE TRUE 2.36 0.00236967 ENSG00000149554 - - 24,0 7,0 0,0,145 0,3,485 0,0,144 0,3,474 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0141,AOGC-02-0459,AOGC-08-0307 80,99,99 chr11:125514501:125514501:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 125514501 125514501 A G snp nonsynonymous SNV CHEK1:NM_001114121:exon11:c.A1196G:p.K399R,CHEK1:NM_001274:exon11:c.A1196G:p.K399R,CHEK1:NM_001244846:exon11:c.A1196G:p.K399R,CHEK1:NM_001114122:exon11:c.A1196G:p.K399R, nonsynonymous SNV CHEK1 missense_variant nonsynonymous SNV ENSG00000149554 PASS FALSE FALSE TRUE TRUE TRUE 5.5 0.000787402 ENSG00000149554:ENST00000428830:exon11:c.A1196G:p.K399R,ENSG00000149554:ENST00000534070:exon11:c.A1196G:p.K399R,ENSG00000149554:ENST00000524737:exon10:c.A1196G:p.K399R,ENSG00000149554:ENST00000438015:exon11:c.A1196G:p.K399R,ENSG00000149554:ENST00000544373:exon11:c.A1196G:p.K399R,ENSG00000149554:ENST00000427383:exon10:c.A1244G:p.K415R, 399 K/R 24,0 23,0 0,0,145 0,1,489 0,0,145 0,1,484 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0137 99 chr11:125525276:125525276:T:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 125525276 125525276 T G snp UTR3 CHEK1 UTR3 CHEK1 3_prime_UTR_variant UTR3 ENSG00000149554 PASS FALSE FALSE TRUE TRUE TRUE 4.84 0.000784929 ENSG00000149554 - - 25,0 13,0 0,1,145 0,0,491 0,1,143 0,0,476 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2812-03B-01W-0728-08 99 chr11:65629694:65629696:CAC:-:indel 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr11 65629694 65629696 CAC - indel nonframeshift deletion MUS81:NM_025128:exon5:c.463_465del:p.155_155del, nonframeshift deletion MUS81 inframe_deletion nonframeshift deletion ENSG00000172732 PASS FALSE FALSE TRUE TRUE TRUE 1.25 0.00235849 ENSG00000172732:ENST00000308110:exon5:c.463_465del:p.155_155del,ENSG00000172732:ENST00000525768:exon4:c.238_240del:p.80_80del,ENSG00000172732:ENST00000533035:exon5:c.238_240del:p.80_80del, 80 H/- 24,0 21,0 0,0,145 0,3,488 0,0,142 0,3,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0105,AOGC-02-0108,AOGC-02-0183 99,99,99 chr11:94194224:94194224:A:-:indel 0.00994037111187031 0.770800627943486 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 94194224 94194224 A - indel intronic MRE11A intronic MRE11A intron_variant,feature_truncation intronic ENSG00000020922 PASS FALSE TRUE TRUE TRUE TRUE 3.19 0.00160514 ENSG00000020922 - - 12,8 7,0 0,2,142 0,0,479 0,2,139 0,0,410 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2878-03A-01W-0732-08,TCGA-AB-2948-03A-01W-0755-09 99,99 chr11:94212931:94212931:-:A:indel:94212930 0.483465585217707 0.0639917996778452 0.0913203800442165 0.0156494522691706 0.0156494522691706 1 1 0 chr11 94212931 94212931 - A indel:94212930 splicing MRE11A(NM_005591:exon6:c.315-4->T,NM_005590:exon6:c.315-4->T) splicing MRE11A splice_region_variant,intron_variant,feature_elongation splicing ENSG00000020922 PASS TRUE TRUE TRUE TRUE TRUE 3.02 0.015748 ENSG00000020922(ENST00000323929:exon6:c.315-4->T,ENST00000407439:exon6:c.324-4->T,ENST00000323977:exon6:c.315-4->T,ENST00000393241:exon6:c.315-4->T,ENST00000540013:exon6:c.315-4->T,ENST00000536754:exon6:c.315-4->T,ENST00000538923:exon6:c.315-4->T) - - 20,20 39,39 1,4,140 0,14,476 1,4,140 0,14,471 1 1 1 1 0 0 1 0 0 1 0 0 1 1 1 1 1 1 0 1 TCGA-AB-2810-03B-01W-0728-08,TCGA-AB-2812-03B-01W-0728-08,TCGA-AB-2840-03D-01W-0755-09,TCGA-AB-2859-03B-01W-0728-08,TCGA-AB-2872-03A-01W-0732-08 99,99,99,99,87 AOGC-02-0013,AOGC-02-0036,AOGC-02-0037,AOGC-02-0095,AOGC-02-0154,AOGC-02-0317,AOGC-02-0525,AOGC-03-0130,AOGC-03-0154,AOGC-03-0165,AOGC-08-0048,AOGC-08-0159,AOGC-08-0186,AOGC-08-0204 0,51,95,3,84,88,99,75,99,99,99,75,24,75 chr11:108150365:108150367:ATC:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108150365 108150367 ATC - indel intronic ATM intronic ATM intron_variant,feature_truncation intronic ENSG00000149311 PASS FALSE FALSE TRUE TRUE TRUE 3.08 0.000786164 ENSG00000149311 - - 23,0 22,0 0,0,146 0,1,489 0,0,145 0,1,450 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0316 99 chr11:108168116:108168117:TA:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108168116 108168117 TA - indel intronic ATM intronic ATM splice_region_variant,intron_variant,feature_truncation intronic ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 3.24 0.000791139 ENSG00000149311 - - 21,0 8,0 0,0,145 0,1,486 0,0,145 0,1,409 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0475 99 chr11:108191989:108191992:TTCT:-:indel 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr11 108191989 108191992 TTCT - indel intronic ATM intronic ATM intron_variant,feature_truncation intronic ENSG00000149311 PASS FALSE TRUE TRUE TRUE TRUE 2.61 0.00157729 ENSG00000149311,ENSG00000166323 - - 21,0 20,0 0,1,144 0,1,488 0,1,144 0,1,468 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2852-03A-01W-0726-08 99 AOGC-08-0060 99 chr11:108202673:108202676:CAAA:-:indel 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr11 108202673 108202676 CAAA - indel frameshift deletion ATM:NM_000051:exon52:c.7697_7700del:p.2566_2567del, frameshift deletion ATM frameshift_variant,feature_truncation frameshift deletion ENSG00000149311 PASS TRUE TRUE TRUE TRUE TRUE 5.28 0.000784929 ENSG00000149311:ENST00000452508:exon53:c.7697_7700del:p.2566_2567del,ENSG00000149311:ENST00000278616:exon52:c.7697_7700del:p.2566_2567del, 2566-2567 - 20,0 20,0 0,1,145 0,0,491 0,1,144 0,0,478 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2875-03A-01W-0732-08 99 chr11:125514290:125514293:AAGA:-:indel 0.717001560156744 -0.0427559247495718 0.117957455113093 0.00860719874804382 0.00860719874804382 1 1 0 chr11 125514290 125514293 AAGA - indel intronic CHEK1 intronic CHEK1 intron_variant,feature_truncation intronic ENSG00000149554 PASS TRUE TRUE TRUE TRUE TRUE 2.72 0.0088 ENSG00000149554 - - 10,0 NA 0,2,135 1,7,480 0,2,121 1,6,466 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 0.0293944758256105 1 0 1 TCGA-AB-2826-03B-01W-0728-08,TCGA-AB-2881-03A-01W-0732-08 99,99 AOGC-02-0092,AOGC-02-0208,AOGC-02-0225,AOGC-02-0274,AOGC-02-0281,AOGC-02-0355,AOGC-08-0081,AOGC-14-0059 99,99,99,99,12,99,99,99 chr13:32906471:32906471:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32906471 32906471 T C snp nonsynonymous SNV BRCA2:NM_000059:exon10:c.T856C:p.S286P, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 1.96 0.000788644 ENSG00000139618:ENST00000530893:exon10:c.T487C:p.S163P,ENSG00000139618:ENST00000544455:exon10:c.T856C:p.S286P,ENSG00000139618:ENST00000380152:exon10:c.T856C:p.S286P, 286 S/P 29,0 21,0 0,1,144 0,0,489 0,1,144 0,0,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2933-03A-01W-0732-08 99 chr13:32906593:32906593:C:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32906593 32906593 C A snp nonsynonymous SNV BRCA2:NM_000059:exon10:c.C978A:p.S326R, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE TRUE TRUE TRUE -2.86 0.000786164 ENSG00000139618:ENST00000530893:exon10:c.C609A:p.S203R,ENSG00000139618:ENST00000544455:exon10:c.C978A:p.S326R,ENSG00000139618:ENST00000380152:exon10:c.C978A:p.S326R, 326 S/R 29,0 12,0 0,1,144 0,0,491 0,1,144 0,0,477 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2939-03A-01W-0745-08 99 chr13:32907042:32907042:C:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32907042 32907042 C G snp nonsynonymous SNV BRCA2:NM_000059:exon10:c.C1427G:p.S476C, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 5.3 0.000786164 ENSG00000139618:ENST00000530893:exon10:c.C1058G:p.S353C,ENSG00000139618:ENST00000544455:exon10:c.C1427G:p.S476C,ENSG00000139618:ENST00000380152:exon10:c.C1427G:p.S476C, 476 S/C 29,0 23,0 0,1,144 0,0,491 0,1,144 0,0,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2836-03B-01W-0728-08 99 chr13:32911295:32911295:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32911295 32911295 G A snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.G2803A:p.D935N, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE TRUE TRUE TRUE -0.456 0.000787402 ENSG00000139618:ENST00000544455:exon11:c.G2803A:p.D935N,ENSG00000139618:ENST00000380152:exon11:c.G2803A:p.D935N, 935 D/N 24,0 12,0 0,0,145 0,1,489 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0198 99 chr13:32912331:32912331:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32912331 32912331 A T snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.A3839T:p.D1280V, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 3.06 0.000796178 ENSG00000139618:ENST00000544455:exon11:c.A3839T:p.D1280V,ENSG00000139618:ENST00000380152:exon11:c.A3839T:p.D1280V, 1280 D/V 10,0 3,0 0,0,142 0,1,485 0,0,120 0,1,449 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0180 99 chr13:32912679:32912679:A:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32912679 32912679 A G snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.A4187G:p.Q1396R, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE FALSE TRUE TRUE 3.56 0.000788644 ENSG00000139618:ENST00000544455:exon11:c.A4187G:p.Q1396R,ENSG00000139618:ENST00000380152:exon11:c.A4187G:p.Q1396R, 1396 Q/R 22,0 11,0 0,1,145 0,0,488 0,1,144 0,0,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2928-03A-01W-0745-08 99 chr13:32912750:32912750:G:T:snp 0.704997875659665 -0.0655608214849913 0.173174436921412 0.00469483568075117 0.00469483568075117 1 1 0 chr13 32912750 32912750 G T snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.G4258T:p.D1420Y, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE FALSE TRUE TRUE 1.06 0.00472441 ENSG00000139618:ENST00000544455:exon11:c.G4258T:p.D1420Y,ENSG00000139618:ENST00000380152:exon11:c.G4258T:p.D1420Y, 1420 D/Y 22,0 11,0 0,1,145 0,5,484 0,1,144 0,4,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2910-03A-01W-0745-08 99 AOGC-02-0136,AOGC-02-0140,AOGC-02-0248,AOGC-03-0060,AOGC-08-0031 71,99,99,99,99 chr13:32913077:32913077:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32913077 32913077 G A snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.G4585A:p.G1529R, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 5.74 0.000787402 ENSG00000139618:ENST00000544455:exon11:c.G4585A:p.G1529R,ENSG00000139618:ENST00000380152:exon11:c.G4585A:p.G1529R, 1529 G/R 29,0 25,0 0,1,144 0,0,490 0,1,144 0,0,476 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2821-03B-01W-0728-08 99 chr13:32913173:32913173:C:A:snp 0.068543172725465 0.384796238244514 0.211261777435397 0.00156494522691706 0.00156494522691706 1 1 0 chr13 32913173 32913173 C A snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.C4681A:p.H1561N, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE FALSE TRUE TRUE 2.52 0.00157978 ENSG00000139618:ENST00000544455:exon11:c.C4681A:p.H1561N,ENSG00000139618:ENST00000380152:exon11:c.C4681A:p.H1561N, 1561 H/N 29,0 25,0 1,0,144 0,0,488 1,0,144 0,0,473 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2812-03B-01W-0728-08 99 chr13:32914132:32914132:T:G:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr13 32914132 32914132 T G snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.T5640G:p.N1880K, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE FALSE TRUE TRUE 1.84 0.00157233 ENSG00000139618:ENST00000544455:exon11:c.T5640G:p.N1880K,ENSG00000139618:ENST00000380152:exon11:c.T5640G:p.N1880K, 1880 N/K 28,0 23,0 0,1,145 0,1,489 0,1,144 0,1,478 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2891-03A-01W-0733-08 96 AOGC-08-0218 99 chr13:32914389:32914389:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32914389 32914389 A G snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.A5897G:p.H1966R, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 2.92 0.000788644 ENSG00000139618:ENST00000544455:exon11:c.A5897G:p.H1966R,ENSG00000139618:ENST00000380152:exon11:c.A5897G:p.H1966R, 1966 H/R 23,0 22,0 0,0,145 0,1,488 0,0,145 0,1,468 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0032 99 chr13:32914592:32914592:C:T:snp 0.370601625965528 0.169716088328076 0.189553423814011 0.00391236306729264 0.00391236306729264 1 1 0 chr13 32914592 32914592 C T snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.C6100T:p.R2034C, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE FALSE TRUE TRUE 1.77 0.00393701 ENSG00000139618:ENST00000544455:exon11:c.C6100T:p.R2034C,ENSG00000139618:ENST00000380152:exon11:c.C6100T:p.R2034C, 2034 R/C 23,0 22,0 0,2,143 0,3,487 0,2,143 0,3,460 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2889-03A-01W-0732-08,TCGA-AB-2919-03A-01W-0745-08 99,99 AOGC-02-0205,AOGC-02-0377,AOGC-08-0051 99,99,99 chr13:32914815:32914815:G:A:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr13 32914815 32914815 G A snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.G6323A:p.R2108H, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE FALSE TRUE TRUE 2.76 0.0015748 ENSG00000139618:ENST00000544455:exon11:c.G6323A:p.R2108H,ENSG00000139618:ENST00000380152:exon11:c.G6323A:p.R2108H, 2108 R/H 23,0 22,0 0,1,144 0,1,489 0,1,144 0,1,476 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2867-03B-01W-0728-08 99 AOGC-08-0197 99 chr13:32914904:32914904:G:T:snp 0.068543172725465 0.384796238244514 0.211261777435397 0.00156494522691706 0.00156494522691706 1 1 0 chr13 32914904 32914904 G T snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.G6412T:p.V2138F, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE FALSE TRUE TRUE -4.6 0.00158479 ENSG00000139618:ENST00000544455:exon11:c.G6412T:p.V2138F,ENSG00000139618:ENST00000380152:exon11:c.G6412T:p.V2138F, 2138 V/F 21,0 9,0 1,0,144 0,0,486 1,0,144 0,0,463 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2812-03B-01W-0728-08 25 chr13:32914947:32914947:C:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32914947 32914947 C A snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.C6455A:p.S2152Y, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 1.12 0.000789889 ENSG00000139618:ENST00000544455:exon11:c.C6455A:p.S2152Y,ENSG00000139618:ENST00000380152:exon11:c.C6455A:p.S2152Y, 2152 S/Y 24,0 21,0 0,1,144 0,0,488 0,1,143 0,0,475 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2957-03A-01W-0733-08 99 chr13:32915313:32915313:G:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr13 32915313 32915313 G T snp nonsynonymous SNV BRCA2:NM_000059:exon11:c.G6821T:p.G2274V, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE TRUE TRUE TRUE 4.79 0.00157233 ENSG00000139618:ENST00000544455:exon11:c.G6821T:p.G2274V,ENSG00000139618:ENST00000380152:exon11:c.G6821T:p.G2274V, 2274 G/V 31,0 21,0 0,0,146 0,2,488 0,0,145 0,2,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0119,AOGC-08-0192 99,99 chr13:32930673:32930673:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32930673 32930673 C T snp nonsynonymous SNV BRCA2:NM_000059:exon15:c.C7544T:p.T2515I, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 4.64 0.000784929 ENSG00000139618:ENST00000544455:exon15:c.C7544T:p.T2515I,ENSG00000139618:ENST00000380152:exon15:c.C7544T:p.T2515I, 2515 T/I 21,0 24,0 0,0,146 0,1,490 0,0,146 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0524 99 chr13:32930694:32930694:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32930694 32930694 C T snp nonsynonymous SNV BRCA2:NM_000059:exon15:c.C7565T:p.S2522F, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 5.48 0.000784929 ENSG00000139618:ENST00000544455:exon15:c.C7565T:p.S2522F,ENSG00000139618:ENST00000380152:exon15:c.C7565T:p.S2522F, 2522 S/F 21,0 24,0 0,0,146 0,1,490 0,0,146 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0063 99 chr13:32930734:32930734:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32930734 32930734 T G snp nonsynonymous SNV BRCA2:NM_000059:exon15:c.T7605G:p.C2535W, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 1.46 0.000784929 ENSG00000139618:ENST00000544455:exon15:c.T7605G:p.C2535W,ENSG00000139618:ENST00000380152:exon15:c.T7605G:p.C2535W, 2535 C/W 21,0 24,0 0,0,146 0,1,490 0,0,145 0,1,474 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0165 99 chr13:32932072:32932072:C:G:snp 0.068543172725465 0.384796238244514 0.211261777435397 0.00156494522691706 0.00156494522691706 1 1 0 chr13 32932072 32932072 C G snp intronic BRCA2 intronic BRCA2 splice_region_variant,intron_variant intronic ENSG00000139618 PASS FALSE FALSE FALSE TRUE TRUE -1.37 0.0015748 ENSG00000139618 - - 31,0 20,0 1,0,145 0,0,489 1,0,144 0,0,434 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2812-03B-01W-0728-08 99 chr13:32937327:32937327:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32937327 32937327 A T snp nonsynonymous SNV BRCA2:NM_000059:exon18:c.A7988T:p.E2663V, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 4.93 0.000787402 ENSG00000139618:ENST00000544455:exon18:c.A7988T:p.E2663V,ENSG00000139618:ENST00000380152:exon18:c.A7988T:p.E2663V, 2663 E/V 36,0 23,0 0,0,145 0,1,489 0,0,145 0,1,453 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0069 99 chr13:32944593:32944593:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32944593 32944593 C T snp nonsynonymous SNV BRCA2:NM_000059:exon19:c.C8386T:p.P2796S, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 2.02 0.000784929 ENSG00000139618:ENST00000544455:exon19:c.C8386T:p.P2796S,ENSG00000139618:ENST00000380152:exon19:c.C8386T:p.P2796S, 2796 P/S 21,0 26,0 0,0,146 0,1,490 0,0,146 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0027 99 chr13:32945172:32945172:A:C:snp 0.704997875659665 -0.0655608214849913 0.173174436921412 0.00469483568075117 0.00469483568075117 1 1 0 chr13 32945172 32945172 A C snp nonsynonymous SNV BRCA2:NM_000059:exon20:c.A8567C:p.E2856A, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE FALSE TRUE TRUE 5.28 0.00471698 ENSG00000139618:ENST00000544455:exon20:c.A8567C:p.E2856A,ENSG00000139618:ENST00000380152:exon20:c.A8567C:p.E2856A,ENSG00000139618:ENST00000528762:exon1:c.A65C:p.E22A, 2856 E/A 31,0 28,0 0,1,144 0,5,486 0,1,144 0,5,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2918-03A-01W-0745-08 99 AOGC-02-0289,AOGC-02-0519,AOGC-02-0536,AOGC-08-0267,AOGC-08-0303 99,99,99,99,99 chr13:32953549:32953549:G:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr13 32953549 32953549 G T snp nonsynonymous SNV BRCA2:NM_000059:exon22:c.G8850T:p.K2950N, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE TRUE TRUE TRUE 1.76 0.00156986 ENSG00000139618:ENST00000544455:exon22:c.G8850T:p.K2950N,ENSG00000139618:ENST00000380152:exon22:c.G8850T:p.K2950N, 2950 K/N 22,0 21,0 0,0,146 0,2,489 0,0,146 0,2,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0099,AOGC-02-0335 99,99 chr13:32954037:32954037:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32954037 32954037 A G snp nonsynonymous SNV BRCA2:NM_000059:exon23:c.A9104G:p.Y3035C, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 4.46 0.000794913 ENSG00000139618:ENST00000544455:exon23:c.A9104G:p.Y3035C,ENSG00000139618:ENST00000380152:exon23:c.A9104G:p.Y3035C, 3035 Y/C 13,0 2,0 0,0,145 0,1,483 0,0,141 0,1,431 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0141 99 chr13:32968933:32968933:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32968933 32968933 G A snp nonsynonymous SNV BRCA2:NM_000059:exon25:c.G9364A:p.A3122T, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 5.89 0.000786164 ENSG00000139618:ENST00000544455:exon25:c.G9364A:p.A3122T,ENSG00000139618:ENST00000380152:exon25:c.G9364A:p.A3122T, 3122 A/T 23,0 21,0 0,0,145 0,1,490 0,0,144 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0203 99 chr13:32968979:32968979:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32968979 32968979 C T snp nonsynonymous SNV BRCA2:NM_000059:exon25:c.C9410T:p.T3137I, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 4.15 0.000786164 ENSG00000139618:ENST00000544455:exon25:c.C9410T:p.T3137I,ENSG00000139618:ENST00000380152:exon25:c.C9410T:p.T3137I, 3137 T/I 23,0 21,0 0,0,145 0,1,490 0,0,144 0,1,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0297 99 chr13:32969073:32969073:A:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32969073 32969073 A T snp splicing BRCA2(NM_000059:exon25:c.9501+3A>T) splicing BRCA2 splice_region_variant,intron_variant splicing ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 2.23 0.000787402 ENSG00000139618(ENST00000380152:exon25:c.9501+3A>T,ENST00000544455:exon25:c.9501+3A>T,ENST00000470094:exon3:c.458+3A>T) - - 23,0 21,0 0,1,144 0,0,490 0,1,143 0,0,459 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2803-03B-01W-0728-08 99 chr13:32971042:32971042:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32971042 32971042 A G snp nonsynonymous SNV BRCA2:NM_000059:exon26:c.A9509G:p.D3170G, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE TRUE TRUE TRUE TRUE 0.419 0.000787402 ENSG00000139618:ENST00000544455:exon26:c.A9509G:p.D3170G,ENSG00000139618:ENST00000380152:exon26:c.A9509G:p.D3170G, 3170 D/G 22,0 21,0 0,0,146 0,1,488 0,0,145 0,1,443 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0132 99 chr13:32972760:32972760:G:A:snp 0.675730396862748 0.102201257861636 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr13 32972760 32972760 G A snp synonymous SNV BRCA2:NM_000059:exon27:c.G10110A:p.R3370R, synonymous SNV BRCA2 synonymous_variant synonymous SNV ENSG00000139618 PASS FALSE FALSE TRUE TRUE TRUE 2.85 0.00236967 ENSG00000139618:ENST00000544455:exon27:c.G10110A:p.R3370R,ENSG00000139618:ENST00000380152:exon27:c.G10110A:p.R3370R, 3370 R 20,0 26,0 0,1,144 0,2,486 0,1,144 0,2,471 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2840-03D-01W-0755-09 99 AOGC-02-0304,AOGC-02-0305 99,99 chr13:32972832:32972832:G:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32972832 32972832 G T snp nonsynonymous SNV BRCA2:NM_000059:exon27:c.G10182T:p.Q3394H, nonsynonymous SNV BRCA2 missense_variant nonsynonymous SNV ENSG00000139618 PASS FALSE FALSE TRUE TRUE TRUE -5.81 0.000789889 ENSG00000139618:ENST00000544455:exon27:c.G10182T:p.Q3394H,ENSG00000139618:ENST00000380152:exon27:c.G10182T:p.Q3394H, 3394 Q/H 20,0 26,0 0,0,146 0,1,486 0,0,145 0,1,465 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0016 54 chr13:32905087:32905087:-:AAG:indel 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr13 32905087 32905087 - AAG indel nonframeshift insertion BRCA2:NM_000059:exon9:c.713_714insAAG:p.E238delinsER, nonframeshift insertion BRCA2 inframe_insertion nonframeshift insertion ENSG00000139618 PASS TRUE TRUE TRUE TRUE TRUE 4.55 0.000787402 ENSG00000139618:ENST00000530893:exon9:c.344_345insAAG:p.E115delinsER,ENSG00000139618:ENST00000544455:exon9:c.713_714insAAG:p.E238delinsER,ENSG00000139618:ENST00000380152:exon9:c.713_714insAAG:p.E238delinsER, 238 E/ER 20,0 10,0 0,1,144 0,0,490 0,1,143 0,0,481 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2841-03B-01W-0728-08 99 chr14:45605264:45605264:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45605264 45605264 G A snp synonymous SNV FANCM:NM_020937:exon1:c.G30A:p.Q10Q, synonymous SNV FANCM regulatory_region_variant synonymous SNV - PASS FALSE TRUE TRUE TRUE TRUE 3.77 0.000786164 ENSG00000187790:ENST00000267430:exon1:c.G30A:p.Q10Q,ENSG00000187790:ENST00000542564:exon1:c.G30A:p.Q10Q,ENSG00000187790:ENST00000556036:exon1:c.G30A:p.Q10Q, - - 30,0 21,0 0,1,145 0,0,490 0,1,144 0,0,455 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2927-03A-01W-0755-09 99 chr14:45605287:45605287:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45605287 45605287 G A snp nonsynonymous SNV FANCM:NM_020937:exon1:c.G53A:p.R18Q, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE TRUE TRUE TRUE TRUE 4.46 0.000788644 ENSG00000187790:ENST00000267430:exon1:c.G53A:p.R18Q,ENSG00000187790:ENST00000542564:exon1:c.G53A:p.R18Q,ENSG00000187790:ENST00000556036:exon1:c.G53A:p.R18Q, 18 R/Q 30,0 21,0 0,0,145 0,1,488 0,0,145 0,1,463 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0441 99 chr14:45605397:45605397:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45605397 45605397 G A snp nonsynonymous SNV FANCM:NM_020937:exon1:c.G163A:p.D55N, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE TRUE TRUE TRUE TRUE 4.99 0.000788644 ENSG00000187790:ENST00000267430:exon1:c.G163A:p.D55N,ENSG00000187790:ENST00000542564:exon1:c.G163A:p.D55N,ENSG00000187790:ENST00000556036:exon1:c.G163A:p.D55N, 55 D/N 25,0 21,0 0,0,145 0,1,488 0,0,145 0,1,484 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0305 99 chr14:45605405:45605405:G:C:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr14 45605405 45605405 G C snp nonsynonymous SNV FANCM:NM_020937:exon1:c.G171C:p.L57F, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE FALSE TRUE TRUE TRUE 1.07 0.00157729 ENSG00000187790:ENST00000267430:exon1:c.G171C:p.L57F,ENSG00000187790:ENST00000542564:exon1:c.G171C:p.L57F,ENSG00000187790:ENST00000556036:exon1:c.G171C:p.L57F, 57 L/F 25,0 21,0 0,0,145 0,2,487 0,0,145 0,2,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0279,AOGC-14-0154 99,99 chr14:45605457:45605457:T:G:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr14 45605457 45605457 T G snp nonsynonymous SNV FANCM:NM_020937:exon1:c.T223G:p.F75V, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS TRUE TRUE TRUE TRUE TRUE 5.32 0.00161812 ENSG00000187790:ENST00000267430:exon1:c.T223G:p.F75V,ENSG00000187790:ENST00000542564:exon1:c.T223G:p.F75V,ENSG00000187790:ENST00000556036:exon1:c.T223G:p.F75V, 75 F/V 36,0 21,0 0,0,145 0,2,471 0,0,145 0,1,462 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0032,AOGC-03-0087 84,49 chr14:45605503:45605503:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45605503 45605503 C T snp nonsynonymous SNV FANCM:NM_020937:exon1:c.C269T:p.P90L, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE TRUE TRUE TRUE TRUE 5.65 0.000784929 ENSG00000187790:ENST00000267430:exon1:c.C269T:p.P90L,ENSG00000187790:ENST00000542564:exon1:c.C269T:p.P90L,ENSG00000187790:ENST00000556036:exon1:c.C269T:p.P90L, 90 P/L 31,0 21,0 0,0,146 0,1,490 0,0,145 0,1,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0126 99 chr14:45606290:45606290:C:T:snp 0.575977326218678 -0.0897377938517171 0.160455166401833 0.0054773082942097 0.0054773082942097 1 1 0 chr14 45606290 45606290 C T snp nonsynonymous SNV FANCM:NM_020937:exon2:c.C527T:p.T176I, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE FALSE FALSE TRUE TRUE 3.13 0.00549451 ENSG00000187790:ENST00000267430:exon2:c.C527T:p.T176I,ENSG00000187790:ENST00000542564:exon2:c.C527T:p.T176I,ENSG00000187790:ENST00000556036:exon2:c.C527T:p.T176I, 176 T/I 21,0 21,0 0,1,145 0,6,485 0,1,144 0,6,475 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2926-03A-01W-0732-08 99 AOGC-02-0010,AOGC-02-0063,AOGC-02-0475,AOGC-03-0118,AOGC-08-0031,AOGC-08-0185 99,99,99,99,99,99 chr14:45620721:45620721:C:T:snp 0.00994037111187031 0.770800627943486 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr14 45620721 45620721 C T snp nonsynonymous SNV FANCM:NM_020937:exon5:c.C1040T:p.P347L, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE FALSE FALSE TRUE TRUE 4.22 0.0015949 ENSG00000187790:ENST00000267430:exon5:c.C1040T:p.P347L,ENSG00000187790:ENST00000542564:exon4:c.C962T:p.P321L,ENSG00000187790:ENST00000556036:exon5:c.C1040T:p.P347L, 347 P/L 23,0 9,0 0,2,143 0,0,482 0,2,143 0,0,403 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2812-03B-01W-0728-08,TCGA-AB-2872-03A-01W-0732-08 99,99 chr14:45623953:45623953:T:C:snp 0.27105525402704 -0.233070866141732 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr14 45623953 45623953 T C snp nonsynonymous SNV FANCM:NM_020937:exon7:c.T1237C:p.Y413H, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE FALSE TRUE TRUE TRUE 4.6 0.00315956 ENSG00000187790:ENST00000267430:exon7:c.T1237C:p.Y413H,ENSG00000187790:ENST00000542564:exon6:c.T1159C:p.Y387H,ENSG00000187790:ENST00000556036:exon7:c.T1237C:p.Y413H, 413 Y/H 30,0 7,0 0,0,146 0,4,483 0,0,145 0,3,452 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0158,AOGC-02-0392,AOGC-02-0427,AOGC-08-0238 99,99,55,30 chr14:45628478:45628478:C:G:snp 0.675730396862748 0.102201257861636 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr14 45628478 45628478 C G snp nonsynonymous SNV FANCM:NM_020937:exon9:c.C1576G:p.L526V, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE FALSE TRUE TRUE TRUE 3.42 0.00236593 ENSG00000187790:ENST00000267430:exon9:c.C1576G:p.L526V,ENSG00000187790:ENST00000556250:exon3:c.C331G:p.L111V,ENSG00000187790:ENST00000542564:exon8:c.C1498G:p.L500V,ENSG00000187790:ENST00000556036:exon9:c.C1576G:p.L526V, 526 L/V 22,0 8,0 0,1,143 0,2,488 0,1,143 0,2,439 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2885-03A-01W-0732-08 99 AOGC-05-0010,AOGC-08-0063 99,99 chr14:45633616:45633616:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45633616 45633616 G A snp nonsynonymous SNV FANCM:NM_020937:exon10:c.G1636A:p.G546S, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE FALSE TRUE TRUE TRUE 6.07 0.000786164 ENSG00000187790:ENST00000267430:exon10:c.G1636A:p.G546S,ENSG00000187790:ENST00000542564:exon9:c.G1558A:p.G520S,ENSG00000187790:ENST00000556036:exon10:c.G1636A:p.G546S, 546 G/S 29,0 27,0 0,1,144 0,0,491 0,1,144 0,0,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2825-03B-01W-0728-08 99 chr14:45633628:45633628:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45633628 45633628 T C snp synonymous SNV FANCM:NM_020937:exon10:c.T1648C:p.L550L, synonymous SNV FANCM intron_variant synonymous SNV ENSG00000187790 PASS TRUE TRUE TRUE TRUE TRUE 3.76 0.000786164 ENSG00000187790:ENST00000267430:exon10:c.T1648C:p.L550L,ENSG00000187790:ENST00000542564:exon9:c.T1570C:p.L524L,ENSG00000187790:ENST00000556036:exon10:c.T1648C:p.L550L, - - 29,0 27,0 0,1,144 0,0,491 0,1,144 0,0,482 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2900-03A-01W-0733-08 99 chr14:45633831:45633831:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45633831 45633831 A G snp intronic FANCM intronic FANCM intron_variant intronic ENSG00000187790 PASS FALSE TRUE TRUE TRUE TRUE 3.16 0.000796178 ENSG00000187790 - - 2,0 4,0 0,0,143 0,1,484 0,0,132 0,1,418 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0025 95 chr14:45644715:45644715:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45644715 45644715 C T snp nonsynonymous SNV FANCM:NM_020937:exon14:c.C2758T:p.P920S, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE TRUE TRUE TRUE TRUE -0.152 0.000793651 ENSG00000187790:ENST00000267430:exon14:c.C2758T:p.P920S,ENSG00000187790:ENST00000556250:exon7:c.C1306T:p.P436S,ENSG00000187790:ENST00000542564:exon13:c.C2680T:p.P894S, 894 P/S 23,0 21,0 0,0,146 0,1,483 0,0,145 0,1,447 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0202 99 chr14:45644816:45644816:A:C:snp 0.866515946988662 -0.0318611987381696 0.189553423814011 0.00391236306729264 0.00391236306729264 1 1 0 chr14 45644816 45644816 A C snp nonsynonymous SNV FANCM:NM_020937:exon14:c.A2859C:p.K953N, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE FALSE TRUE TRUE TRUE 1.19 0.00396825 ENSG00000187790:ENST00000267430:exon14:c.A2859C:p.K953N,ENSG00000187790:ENST00000556250:exon7:c.A1407C:p.K469N,ENSG00000187790:ENST00000542564:exon13:c.A2781C:p.K927N, 927 K/N 23,0 21,0 0,1,144 0,4,481 0,1,144 0,4,438 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2802-03B-01W-0728-08 99 AOGC-02-0031,AOGC-02-0396,AOGC-08-0186,AOGC-08-0205 90,12,99,99 chr14:45645504:45645504:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45645504 45645504 T C snp synonymous SNV FANCM:NM_020937:exon14:c.T3547C:p.L1183L, synonymous SNV FANCM synonymous_variant synonymous SNV ENSG00000187790 PASS FALSE FALSE FALSE TRUE TRUE 2.88 0.000787402 ENSG00000187790:ENST00000267430:exon14:c.T3547C:p.L1183L,ENSG00000187790:ENST00000556250:exon7:c.T2095C:p.L699L,ENSG00000187790:ENST00000542564:exon13:c.T3469C:p.L1157L, 116 L 21,0 22,0 0,1,144 0,0,490 0,1,144 0,0,487 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2810-03B-01W-0728-08 99 chr14:45646186:45646186:T:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45646186 45646186 T G snp intronic FANCM intronic FANCM splice_region_variant,intron_variant intronic ENSG00000187790 PASS FALSE FALSE FALSE TRUE TRUE 0.491 0.000833333 ENSG00000187790 - - 29,0 12,0 0,1,144 0,0,455 0,1,144 0,0,404 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2810-03B-01W-0728-08 99 chr14:45653079:45653079:G:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr14 45653079 45653079 G A snp nonsynonymous SNV FANCM:NM_020937:exon17:c.G4489A:p.V1497I, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE FALSE TRUE TRUE TRUE 2.28 0.00156986 ENSG00000187790:ENST00000267430:exon17:c.G4489A:p.V1497I,ENSG00000187790:ENST00000556250:exon10:c.G3037A:p.V1013I,ENSG00000187790:ENST00000542564:exon16:c.G4411A:p.V1471I, 430 V/I 22,0 22,0 0,0,146 0,2,489 0,0,145 0,2,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0284,AOGC-14-0093 99,69 chr14:45665603:45665603:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 45665603 45665603 G A snp nonsynonymous SNV FANCM:NM_020937:exon21:c.G5569A:p.V1857M, nonsynonymous SNV FANCM missense_variant nonsynonymous SNV ENSG00000187790 PASS FALSE TRUE TRUE TRUE TRUE 4.38 0.000784929 ENSG00000187790:ENST00000267430:exon21:c.G5569A:p.V1857M,ENSG00000187790:ENST00000556250:exon14:c.G4117A:p.V1373M,ENSG00000187790:ENST00000542564:exon20:c.G5491A:p.V1831M,ENSG00000187790:ENST00000557110:exon1:c.G229A:p.V77M, 825 V/M 21,0 20,0 0,0,146 0,1,490 0,0,146 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0297 99 chr14:68292119:68292119:T:C:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr14 68292119 68292119 T C snp intronic RAD51B intronic RAD51B intron_variant intronic ENSG00000182185 PASS FALSE FALSE TRUE TRUE TRUE 2.78 0.00158228 ENSG00000182185 - - 20,0 8,0 0,0,145 0,2,485 0,0,141 0,2,408 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0098,AOGC-02-0525 99,99 chr14:68292146:68292146:T:C:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr14 68292146 68292146 T C snp intronic RAD51B intronic RAD51B intron_variant intronic ENSG00000182185 PASS FALSE TRUE TRUE TRUE TRUE 3.29 0.00156986 ENSG00000182185 - - 20,0 22,0 0,1,145 0,1,490 0,1,144 0,1,445 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2847-03B-01W-0728-08 99 AOGC-02-0345 72 chr14:68301967:68301967:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 68301967 68301967 A G snp intronic RAD51B intronic RAD51B intron_variant intronic ENSG00000182185 PASS FALSE TRUE TRUE TRUE TRUE 4.15 0.000788644 ENSG00000182185 - - 21,0 21,0 0,0,145 0,1,488 0,0,145 0,1,462 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0048 99 chr14:68331840:68331840:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 68331840 68331840 G A snp nonsynonymous SNV RAD51B:NM_133509:exon5:c.G436A:p.A146T,RAD51B:NM_002877:exon5:c.G436A:p.A146T,RAD51B:NM_133510:exon5:c.G436A:p.A146T, nonsynonymous SNV RAD51B missense_variant nonsynonymous SNV ENSG00000182185 PASS FALSE FALSE TRUE TRUE TRUE 5.21 0.000787402 ENSG00000182185:ENST00000390683:exon4:c.G436A:p.A146T,ENSG00000182185:ENST00000487270:exon5:c.G436A:p.A146T,ENSG00000182185:ENST00000471583:exon5:c.G436A:p.A146T,ENSG00000182185:ENST00000488612:exon5:c.G436A:p.A146T,ENSG00000182185:ENST00000487861:exon5:c.G436A:p.A146T, 146 A/T 20,0 21,0 0,0,145 0,1,489 0,0,145 0,1,441 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0311 99 chr14:68353784:68353784:G:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr14 68353784 68353784 G T snp nonsynonymous SNV RAD51B:NM_133509:exon7:c.G619T:p.V207L,RAD51B:NM_002877:exon7:c.G619T:p.V207L,RAD51B:NM_133510:exon7:c.G619T:p.V207L, nonsynonymous SNV RAD51B missense_variant nonsynonymous SNV ENSG00000182185 PASS FALSE FALSE FALSE TRUE TRUE 4.78 0.00157729 ENSG00000182185:ENST00000390683:exon6:c.G619T:p.V207L,ENSG00000182185:ENST00000487270:exon7:c.G619T:p.V207L,ENSG00000182185:ENST00000471583:exon7:c.G619T:p.V207L,ENSG00000182185:ENST00000488612:exon7:c.G619T:p.V207L,ENSG00000182185:ENST00000487861:exon7:c.G619T:p.V207L, 207 V/L 20,0 23,0 0,0,145 0,2,487 0,0,145 0,2,470 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0207,AOGC-02-0264 99,99 chr14:68758762:68758762:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 68758762 68758762 C T snp intronic RAD51B intronic RAD51B regulatory_region_variant intronic - PASS FALSE TRUE TRUE TRUE TRUE 4.76 0.000786164 ENSG00000182185 - - 33,0 8,0 0,0,145 0,1,490 0,0,145 0,1,486 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0106 99 chr14:104174889:104174891:AGG:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr14 104174889 104174891 AGG - indel nonframeshift deletion XRCC3:NM_001100118:exon4:c.161_163del:p.54_55del,XRCC3:NM_005432:exon5:c.161_163del:p.54_55del,XRCC3:NM_001100119:exon5:c.161_163del:p.54_55del, nonframeshift deletion XRCC3 inframe_deletion nonframeshift deletion ENSG00000126215 PASS TRUE TRUE TRUE TRUE TRUE 3.68 0.000789889 ENSG00000126215:ENST00000555055:exon5:c.161_163del:p.54_55del,ENSG00000126215:ENST00000553264:exon3:c.161_163del:p.54_55del,ENSG00000126215:ENST00000555964:exon4:c.161_163del:p.54_55del,ENSG00000126215:ENST00000352127:exon4:c.161_163del:p.54_55del,ENSG00000126215:ENST00000553361:exon4:c.161_163del:p.54_55del,ENSG00000126215:ENST00000554913:exon5:c.161_163del:p.54_55del,ENSG00000126215:ENST00000556980:exon5:c.161_163del:p.54_55del,ENSG00000126215:ENST00000445556:exon4:c.161_163del:p.54_55del,ENSG00000126215:ENST00000557439:exon5:c.161_163del:p.54_55del,ENSG00000126215:ENST00000556682:exon4:c.161_163del:p.54_55del, 54-55 SL/L 22,0 9,0 0,0,142 0,1,490 0,0,141 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0120 99 chr15:31197015:31197015:T:G:snp 0.202168134675384 0.270078740157481 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr15 31197015 31197015 T G snp nonsynonymous SNV FAN1:NM_001146095:exon2:c.T149G:p.M50R,FAN1:NM_001146094:exon2:c.T149G:p.M50R,FAN1:NM_014967:exon2:c.T149G:p.M50R,FAN1:NM_001146096:exon2:c.T149G:p.M50R, nonsynonymous SNV FAN1 missense_variant nonsynonymous SNV ENSG00000198690 PASS FALSE FALSE TRUE TRUE TRUE 5.15 0.00314961 ENSG00000198690:ENST00000561594:exon2:c.T149G:p.M50R,ENSG00000198690:ENST00000561607:exon2:c.T149G:p.M50R,ENSG00000198690:ENST00000362065:exon2:c.T149G:p.M50R,ENSG00000198690:ENST00000565280:exon2:c.T149G:p.M50R,ENSG00000198690:ENST00000565466:exon2:c.T149G:p.M50R, 50 M/R 21,0 17,0 0,2,142 0,2,489 0,2,142 0,2,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2833-03B-01W-0728-08,TCGA-AB-2860-03B-01W-0728-08 99,99 AOGC-02-0142,AOGC-05-0001 99,99 chr15:31197040:31197040:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 31197040 31197040 G A snp synonymous SNV FAN1:NM_001146095:exon2:c.G174A:p.R58R,FAN1:NM_001146094:exon2:c.G174A:p.R58R,FAN1:NM_014967:exon2:c.G174A:p.R58R,FAN1:NM_001146096:exon2:c.G174A:p.R58R, synonymous SNV FAN1 intron_variant synonymous SNV ENSG00000198690 PASS FALSE FALSE TRUE TRUE TRUE 2.16 0.000787402 ENSG00000198690:ENST00000561594:exon2:c.G174A:p.R58R,ENSG00000198690:ENST00000561607:exon2:c.G174A:p.R58R,ENSG00000198690:ENST00000362065:exon2:c.G174A:p.R58R,ENSG00000198690:ENST00000565280:exon2:c.G174A:p.R58R,ENSG00000198690:ENST00000565466:exon2:c.G174A:p.R58R, - - 21,0 17,0 0,0,144 0,1,490 0,0,144 0,1,490 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0238 99 chr15:31197300:31197300:G:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr15 31197300 31197300 G A snp nonsynonymous SNV FAN1:NM_001146095:exon2:c.G434A:p.R145H,FAN1:NM_001146094:exon2:c.G434A:p.R145H,FAN1:NM_014967:exon2:c.G434A:p.R145H,FAN1:NM_001146096:exon2:c.G434A:p.R145H, nonsynonymous SNV FAN1 missense_variant nonsynonymous SNV ENSG00000198690 PASS FALSE FALSE TRUE TRUE TRUE -7.76 0.00157233 ENSG00000198690:ENST00000561594:exon2:c.G434A:p.R145H,ENSG00000198690:ENST00000561607:exon2:c.G434A:p.R145H,ENSG00000198690:ENST00000362065:exon2:c.G434A:p.R145H,ENSG00000198690:ENST00000565280:exon2:c.G434A:p.R145H,ENSG00000198690:ENST00000565466:exon2:c.G434A:p.R145H, 145 R/H 21,0 25,0 0,0,145 0,2,489 0,0,145 0,2,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0317,AOGC-03-0032 99,99 chr15:31197584:31197584:G:A:snp 0.118415338115024 -0.234548335974643 0.15021094947569 0.00625978090766823 0.00625978090766823 1 1 0 chr15 31197584 31197584 G A snp nonsynonymous SNV FAN1:NM_001146095:exon2:c.G718A:p.E240K,FAN1:NM_001146094:exon2:c.G718A:p.E240K,FAN1:NM_014967:exon2:c.G718A:p.E240K,FAN1:NM_001146096:exon2:c.G718A:p.E240K, nonsynonymous SNV FAN1 missense_variant nonsynonymous SNV ENSG00000198690 PASS FALSE FALSE FALSE TRUE TRUE 4.15 0.00628931 ENSG00000198690:ENST00000561594:exon2:c.G718A:p.E240K,ENSG00000198690:ENST00000561607:exon2:c.G718A:p.E240K,ENSG00000198690:ENST00000362065:exon2:c.G718A:p.E240K,ENSG00000198690:ENST00000565280:exon2:c.G718A:p.E240K,ENSG00000198690:ENST00000565466:exon2:c.G718A:p.E240K, 240 E/K 16,0 10,0 0,0,145 0,8,483 0,0,145 0,7,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0027,AOGC-02-0304,AOGC-02-0424,AOGC-03-0172,AOGC-08-0060,AOGC-08-0163,AOGC-08-0237,AOGC-08-0301 13,99,99,99,99,99,99,99 chr15:31197995:31197995:C:T:snp 0.214568483133726 0.199141048824594 0.160455166401833 0.0054773082942097 0.0054773082942097 1 1 0 chr15 31197995 31197995 C T snp nonsynonymous SNV FAN1:NM_001146095:exon2:c.C1129T:p.R377W,FAN1:NM_001146094:exon2:c.C1129T:p.R377W,FAN1:NM_014967:exon2:c.C1129T:p.R377W,FAN1:NM_001146096:exon2:c.C1129T:p.R377W, nonsynonymous SNV FAN1 missense_variant nonsynonymous SNV ENSG00000198690 PASS FALSE FALSE FALSE TRUE TRUE -1.21 0.0055205 ENSG00000198690:ENST00000561594:exon2:c.C1129T:p.R377W,ENSG00000198690:ENST00000561607:exon2:c.C1129T:p.R377W,ENSG00000198690:ENST00000362065:exon2:c.C1129T:p.R377W,ENSG00000198690:ENST00000565280:exon2:c.C1129T:p.R377W,ENSG00000198690:ENST00000565466:exon2:c.C1129T:p.R377W, 377 R/W 23,0 22,0 0,3,142 0,4,485 0,3,142 0,3,470 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2826-03B-01W-0728-08,TCGA-AB-2848-03B-01W-0728-08,TCGA-AB-2898-03A-01W-0733-08 99,99,99 AOGC-02-0012,AOGC-02-0254,AOGC-02-0361,AOGC-14-0171 99,94,26,99 chr15:31210304:31210304:G:A:snp 0.000586075755397477 -0.245847176079733 0.0715092390698737 0.0289514866979656 0.0289514866979656 1 1 0 chr15 31210304 31210304 G A snp intronic FAN1 intronic FAN1 intron_variant intronic ENSG00000198690 PASS TRUE TRUE TRUE TRUE TRUE 2.62 0.0294118 ENSG00000198690 - - 29,0 32,0 0,0,145 0,37,447 0,0,144 0,19,412 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0147,AOGC-02-0155,AOGC-02-0202,AOGC-02-0243,AOGC-02-0254,AOGC-02-0304,AOGC-02-0330,AOGC-02-0341,AOGC-02-0342,AOGC-02-0356,AOGC-02-0386,AOGC-02-0388,AOGC-02-0409,AOGC-02-0411,AOGC-02-0475,AOGC-03-0026,AOGC-03-0035,AOGC-03-0116,AOGC-03-0123,AOGC-03-0154,AOGC-03-0174,AOGC-08-0006,AOGC-08-0051,AOGC-08-0066,AOGC-08-0091,AOGC-08-0106,AOGC-08-0145,AOGC-08-0185,AOGC-08-0234,AOGC-08-0242,AOGC-08-0243,AOGC-08-0253,AOGC-08-0279,AOGC-08-0285,AOGC-14-0093,AOGC-14-0326,AOGC-14-0425 23,34,7,11,83,17,19,6,5,26,60,33,21,19,35,9,4,2,40,49,23,3,13,10,3,47,65,17,57,40,6,43,19,20,43,44,11 chr15:31212744:31212744:T:C:snp 0.878941044942029 0.0187400318979274 0.123037322324538 0.00938967136150235 0.00938967136150235 1 1 0 chr15 31212744 31212744 T C snp splicing FAN1(NM_014967:exon7:c.1944-4T>C) splicing FAN1 splice_region_variant,intron_variant splicing ENSG00000198690 PASS FALSE FALSE FALSE TRUE TRUE 4.48 0.00943396 ENSG00000198690(ENST00000362065:exon7:c.1944-4T>C,ENST00000565280:exon8:c.2078-4T>C) - - 29,0 23,0 0,3,142 0,9,482 0,3,142 0,9,478 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2904-03A-01W-0732-08,TCGA-AB-2919-03A-01W-0745-08,TCGA-AB-2940-03A-01W-0733-08 99,99,99 AOGC-02-0029,AOGC-02-0405,AOGC-02-0466,AOGC-03-0091,AOGC-05-0008,AOGC-08-0032,AOGC-08-0106,AOGC-08-0210,AOGC-08-0302 99,99,99,99,74,99,99,99,99 chr15:31212765:31212765:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 31212765 31212765 C T snp nonsynonymous SNV FAN1:NM_014967:exon7:c.C1961T:p.P654L, nonsynonymous SNV FAN1 missense_variant nonsynonymous SNV ENSG00000198690 PASS FALSE FALSE TRUE TRUE TRUE 5.7 0.000786164 ENSG00000198690:ENST00000362065:exon7:c.C1961T:p.P654L, 654 P/L 29,0 23,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0229 99 chr15:31217417:31217417:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 31217417 31217417 C T snp stopgain SNV FAN1:NM_014967:exon9:c.C2260T:p.R754X, stopgain SNV FAN1 stop_gained stopgain SNV ENSG00000198690 PASS TRUE TRUE TRUE TRUE TRUE 3.55 0.000787402 ENSG00000198690:ENST00000362065:exon9:c.C2260T:p.R754X, 754 R/* 25,0 23,0 0,1,144 0,0,490 0,1,144 0,0,476 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2890-03A-01W-0732-08 99 chr15:31220857:31220857:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 31220857 31220857 C T snp stopgain SNV FAN1:NM_014967:exon11:c.C2590T:p.Q864X, stopgain SNV FAN1 stop_gained,splice_region_variant stopgain SNV ENSG00000198690 PASS FALSE TRUE TRUE TRUE TRUE 5.35 0.000786164 ENSG00000198690:ENST00000362065:exon11:c.C2590T:p.Q864X, 864 Q/* 61,0 28,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0317 99 chr15:31221527:31221527:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 31221527 31221527 C T snp nonsynonymous SNV FAN1:NM_014967:exon12:c.C2714T:p.T905M, nonsynonymous SNV FAN1 missense_variant nonsynonymous SNV ENSG00000198690 PASS FALSE TRUE TRUE TRUE TRUE 2 0.000787402 ENSG00000198690:ENST00000362065:exon12:c.C2714T:p.T905M, 905 T/M 20,0 21,0 0,0,144 0,1,490 0,0,144 0,1,467 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0054 99 chr15:31222790:31222790:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 31222790 31222790 C T snp synonymous SNV FAN1:NM_014967:exon13:c.C2832T:p.C944C, synonymous SNV FAN1 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000198690 PASS FALSE FALSE TRUE TRUE TRUE 3.56 0.000786164 ENSG00000198690:ENST00000362065:exon13:c.C2832T:p.C944C, - - 21,0 22,0 0,0,145 0,1,490 0,0,144 0,1,482 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0031 99 chr15:40990873:40990873:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 40990873 40990873 A G snp intronic RAD51 intronic RAD51 intron_variant,NMD_transcript_variant intronic ENSG00000051180 PASS FALSE TRUE TRUE TRUE TRUE 2.33 0.000791139 ENSG00000051180 - - 12,0 2,0 0,0,142 0,1,489 0,0,123 0,1,445 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0056 52 chr15:41001295:41001295:C:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr15 41001295 41001295 C T snp nonsynonymous SNV RAD51:NM_001164270:exon5:c.C416T:p.T139M,RAD51:NM_001164269:exon5:c.C419T:p.T140M,RAD51:NM_133487:exon5:c.C419T:p.T140M,RAD51:NM_002875:exon5:c.C416T:p.T139M, nonsynonymous SNV RAD51 missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000051180 PASS FALSE FALSE TRUE TRUE TRUE 5.72 0.00157233 ENSG00000051180:ENST00000527860:exon5:c.C416T:p.T139M,ENSG00000051180:ENST00000423169:exon5:c.C416T:p.T139M,ENSG00000051180:ENST00000525066:exon5:c.C416T:p.T139M,ENSG00000051180:ENST00000531277:exon3:c.C298T:p.R100C,ENSG00000051180:ENST00000532743:exon5:c.C419T:p.T140M,ENSG00000051180:ENST00000382643:exon5:c.C419T:p.T140M,ENSG00000051180:ENST00000267868:exon5:c.C416T:p.T139M, 100 R/C 27,0 28,0 0,0,145 0,2,489 0,0,145 0,2,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0065,AOGC-02-0069 99,99 chr15:41011016:41011016:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 41011016 41011016 G A snp nonsynonymous SNV RAD51:NM_001164270:exon6:c.G449A:p.R150Q,RAD51:NM_001164269:exon6:c.G452A:p.R151Q,RAD51:NM_133487:exon6:c.G452A:p.R151Q,RAD51:NM_002875:exon6:c.G449A:p.R150Q, nonsynonymous SNV RAD51 missense_variant nonsynonymous SNV ENSG00000051180 PASS FALSE FALSE TRUE TRUE TRUE 5.63 0.000784929 ENSG00000051180:ENST00000527860:exon6:c.G449A:p.R150Q,ENSG00000051180:ENST00000423169:exon6:c.G449A:p.R150Q,ENSG00000051180:ENST00000532743:exon6:c.G452A:p.R151Q,ENSG00000051180:ENST00000382643:exon6:c.G452A:p.R151Q,ENSG00000051180:ENST00000267868:exon6:c.G449A:p.R150Q, 150 R/Q 25,0 22,0 0,1,145 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2869-03A-01W-0761-09 99 chr15:41021729:41021729:C:G:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr15 41021729 41021729 C G snp nonsynonymous SNV RAD51:NM_001164270:exon8:c.C671G:p.A224G,RAD51:NM_001164269:exon8:c.C674G:p.A225G,RAD51:NM_133487:exon8:c.C674G:p.A225G,RAD51:NM_002875:exon8:c.C671G:p.A224G, nonsynonymous SNV RAD51 missense_variant nonsynonymous SNV ENSG00000051180 PASS FALSE TRUE TRUE TRUE TRUE 5.72 0.00156986 ENSG00000051180:ENST00000423169:exon8:c.C671G:p.A224G,ENSG00000051180:ENST00000532743:exon8:c.C674G:p.A225G,ENSG00000051180:ENST00000382643:exon8:c.C674G:p.A225G,ENSG00000051180:ENST00000267868:exon8:c.C671G:p.A224G,ENSG00000051180:ENST00000557850:exon6:c.C380G:p.A127G, 224 A/G 32,0 23,0 0,1,145 0,1,490 0,1,144 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2894-03A-01W-0733-08 99 AOGC-02-0006 2 chr15:41022071:41022071:C:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 41022071 41022071 C G snp nonsynonymous SNV RAD51:NM_001164269:exon9:c.C798G:p.I266M,RAD51:NM_133487:exon9:c.C798G:p.I266M,RAD51:NM_002875:exon9:c.C795G:p.I265M, nonsynonymous SNV RAD51 missense_variant nonsynonymous SNV ENSG00000051180 PASS TRUE TRUE TRUE TRUE TRUE 4.08 0.000784929 ENSG00000051180:ENST00000532743:exon9:c.C798G:p.I266M,ENSG00000051180:ENST00000382643:exon9:c.C798G:p.I266M,ENSG00000051180:ENST00000267868:exon9:c.C795G:p.I265M,ENSG00000051180:ENST00000557850:exon7:c.C504G:p.I168M, 266 I/M 32,0 25,0 0,1,145 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2910-03A-01W-0745-08 99 chr15:41022106:41022106:C:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr15 41022106 41022106 C T snp nonsynonymous SNV RAD51:NM_001164269:exon9:c.C833T:p.A278V,RAD51:NM_133487:exon9:c.C833T:p.A278V,RAD51:NM_002875:exon9:c.C830T:p.A277V, nonsynonymous SNV RAD51 missense_variant nonsynonymous SNV ENSG00000051180 PASS FALSE FALSE TRUE TRUE TRUE 5.03 0.00156986 ENSG00000051180:ENST00000532743:exon9:c.C833T:p.A278V,ENSG00000051180:ENST00000382643:exon9:c.C833T:p.A278V,ENSG00000051180:ENST00000267868:exon9:c.C830T:p.A277V,ENSG00000051180:ENST00000557850:exon7:c.C539T:p.A180V, 278 A/V 32,0 25,0 0,0,146 0,2,489 0,0,145 0,2,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0249,AOGC-02-0250 99,99 chr15:89804819:89804819:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89804819 89804819 C T snp nonsynonymous SNV FANCI:NM_001113378:exon5:c.C292T:p.H98Y,FANCI:NM_018193:exon5:c.C292T:p.H98Y, nonsynonymous SNV FANCI missense_variant nonsynonymous SNV ENSG00000140525 PASS FALSE FALSE TRUE TRUE TRUE 4.36 0.000786164 ENSG00000140525:ENST00000310775:exon5:c.C292T:p.H98Y,ENSG00000140525:ENST00000447611:exon5:c.C292T:p.H98Y,ENSG00000140525:ENST00000567996:exon7:c.C292T:p.H98Y,ENSG00000140525:ENST00000567891:exon5:c.C292T:p.H98Y,ENSG00000140525:ENST00000565255:exon5:c.C292T:p.H98Y,ENSG00000140525:ENST00000564920:exon6:c.C292T:p.H98Y,ENSG00000140525:ENST00000563250:exon5:c.C292T:p.H98Y,ENSG00000140525:ENST00000300027:exon5:c.C292T:p.H98Y, 98 H/Y 23,0 24,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0426 99 chr15:89805046:89805046:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89805046 89805046 T G snp intronic FANCI intronic FANCI splice_region_variant,intron_variant intronic ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE 2.55 0.000786164 ENSG00000140525 - - 23,0 24,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0345 99 chr15:89805154:89805154:C:T:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr15 89805154 89805154 C T snp intronic FANCI intronic FANCI intron_variant intronic ENSG00000140525 PASS FALSE FALSE TRUE TRUE TRUE 3.58 0.0015748 ENSG00000140525 - - 20,0 18,0 0,1,143 0,1,490 0,1,141 0,1,486 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2912-03A-01W-0732-08 99 AOGC-02-0056 99 chr15:89807187:89807187:G:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89807187 89807187 G T snp nonsynonymous SNV FANCI:NM_001113378:exon8:c.G599T:p.S200I,FANCI:NM_018193:exon8:c.G599T:p.S200I, nonsynonymous SNV FANCI missense_variant nonsynonymous SNV ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE -11.8 0.000786164 ENSG00000140525:ENST00000310775:exon8:c.G599T:p.S200I,ENSG00000140525:ENST00000447611:exon8:c.G599T:p.S200I,ENSG00000140525:ENST00000451393:exon10:c.G62T:p.S21I,ENSG00000140525:ENST00000567996:exon10:c.G599T:p.S200I,ENSG00000140525:ENST00000570225:exon3:c.G137T:p.S46I,ENSG00000140525:ENST00000565255:exon8:c.G599T:p.S200I,ENSG00000140525:ENST00000563250:exon8:c.G599T:p.S200I,ENSG00000140525:ENST00000300027:exon8:c.G599T:p.S200I, 200 S/I 27,0 20,0 0,0,145 0,1,490 0,0,145 0,1,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0224 99 chr15:89807808:89807808:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89807808 89807808 A G snp nonsynonymous SNV FANCI:NM_001113378:exon9:c.A725G:p.K242R,FANCI:NM_018193:exon9:c.A725G:p.K242R, nonsynonymous SNV FANCI missense_variant nonsynonymous SNV ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE 2.46 0.000786164 ENSG00000140525:ENST00000310775:exon9:c.A725G:p.K242R,ENSG00000140525:ENST00000447611:exon9:c.A725G:p.K242R,ENSG00000140525:ENST00000451393:exon11:c.A188G:p.K63R,ENSG00000140525:ENST00000567996:exon11:c.A725G:p.K242R,ENSG00000140525:ENST00000570225:exon4:c.A263G:p.K88R,ENSG00000140525:ENST00000300027:exon9:c.A725G:p.K242R, 63 K/R 29,0 21,0 0,0,145 0,1,490 0,0,145 0,1,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0133 99 chr15:89807836:89807836:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89807836 89807836 C T snp synonymous SNV FANCI:NM_001113378:exon9:c.C753T:p.D251D,FANCI:NM_018193:exon9:c.C753T:p.D251D, synonymous SNV FANCI splice_region_variant,synonymous_variant synonymous SNV ENSG00000140525 PASS FALSE FALSE TRUE TRUE TRUE 2.35 0.000786164 ENSG00000140525:ENST00000310775:exon9:c.C753T:p.D251D,ENSG00000140525:ENST00000447611:exon9:c.C753T:p.D251D,ENSG00000140525:ENST00000451393:exon11:c.C216T:p.D72D,ENSG00000140525:ENST00000567996:exon11:c.C753T:p.D251D,ENSG00000140525:ENST00000570225:exon4:c.C291T:p.D97D,ENSG00000140525:ENST00000300027:exon9:c.C753T:p.D251D, 78 D 29,0 21,0 0,0,145 0,1,490 0,0,145 0,1,478 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0004 99 chr15:89819932:89819932:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89819932 89819932 G C snp intronic FANCI intronic FANCI intron_variant,NMD_transcript_variant intronic ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE 3.47 0.000787402 ENSG00000140525 - - 31,0 22,0 0,0,145 0,1,489 0,0,145 0,1,472 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0070 99 chr15:89820079:89820079:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89820079 89820079 A G snp nonsynonymous SNV FANCI:NM_001113378:exon13:c.A1250G:p.H417R,FANCI:NM_018193:exon13:c.A1250G:p.H417R, nonsynonymous SNV FANCI missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE 4.61 0.000786164 ENSG00000140525:ENST00000310775:exon13:c.A1250G:p.H417R,ENSG00000140525:ENST00000447611:exon13:c.A1250G:p.H417R,ENSG00000140525:ENST00000300027:exon13:c.A1250G:p.H417R, 417 H/R 31,0 22,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0519 99 chr15:89820093:89820093:G:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr15 89820093 89820093 G A snp nonsynonymous SNV FANCI:NM_001113378:exon13:c.G1264A:p.G422R,FANCI:NM_018193:exon13:c.G1264A:p.G422R, nonsynonymous SNV FANCI missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000140525 PASS FALSE FALSE TRUE TRUE TRUE 5.73 0.00157233 ENSG00000140525:ENST00000310775:exon13:c.G1264A:p.G422R,ENSG00000140525:ENST00000447611:exon13:c.G1264A:p.G422R,ENSG00000140525:ENST00000300027:exon13:c.G1264A:p.G422R, 422 G/R 31,0 22,0 0,0,145 0,2,489 0,0,145 0,2,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0070,AOGC-02-0411 99,99 chr15:89825056:89825056:A:G:snp 0.675730396862748 0.102201257861636 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr15 89825056 89825056 A G snp nonsynonymous SNV FANCI:NM_001113378:exon16:c.A1573G:p.M525V,FANCI:NM_018193:exon16:c.A1573G:p.M525V, nonsynonymous SNV FANCI missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000140525 PASS FALSE FALSE FALSE TRUE TRUE 4.67 0.00235849 ENSG00000140525:ENST00000310775:exon16:c.A1573G:p.M525V,ENSG00000140525:ENST00000447611:exon16:c.A1573G:p.M525V,ENSG00000140525:ENST00000300027:exon16:c.A1573G:p.M525V, 525 M/V 29,0 22,0 0,1,144 0,2,489 0,1,144 0,2,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2927-03A-01W-0755-09 99 AOGC-02-0315,AOGC-14-0437 99,99 chr15:89826299:89826299:T:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89826299 89826299 T A snp intronic FANCI intronic FANCI non_coding_exon_variant,nc_transcript_variant intronic ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE 3.04 0.000792393 ENSG00000140525 - - 8,0 7,0 0,0,145 0,1,485 0,0,141 0,1,396 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0535 86 chr15:89826352:89826352:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89826352 89826352 C G snp intronic FANCI intronic FANCI non_coding_exon_variant,nc_transcript_variant intronic ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE 3.06 0.000787402 ENSG00000140525 - - 25,0 24,0 0,0,145 0,1,489 0,0,145 0,1,458 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0147 99 chr15:89848640:89848640:T:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89848640 89848640 T G snp nonsynonymous SNV FANCI:NM_001113378:exon30:c.T3255G:p.C1085W,FANCI:NM_018193:exon29:c.T3075G:p.C1025W, nonsynonymous SNV FANCI missense_variant,splice_region_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE 3.62 0.000786164 ENSG00000140525:ENST00000310775:exon30:c.T3255G:p.C1085W,ENSG00000140525:ENST00000447611:exon29:c.T3075G:p.C1025W,ENSG00000140525:ENST00000300027:exon29:c.T3075G:p.C1025W, 1025 C/W 28,0 26,0 0,1,144 0,0,491 0,1,144 0,0,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2839-03B-01W-0728-08 99 chr15:89848731:89848731:G:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89848731 89848731 G T snp intronic FANCI intronic FANCI intron_variant,NMD_transcript_variant intronic ENSG00000140525 PASS TRUE TRUE TRUE TRUE TRUE 2.87 0.0008 ENSG00000140525 - - 31,0 16,0 0,1,144 0,0,480 0,1,143 0,0,467 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2848-03B-01W-0728-08 96 chr15:89850836:89850836:T:C:snp 0.117699294654503 0.270932069510269 0.173174436921412 0.00469483568075117 0.00469483568075117 1 1 0 chr15 89850836 89850836 T C snp intronic FANCI intronic FANCI splice_region_variant,intron_variant,NMD_transcript_variant intronic ENSG00000140525 PASS FALSE FALSE TRUE TRUE TRUE 1.56 0.00471698 ENSG00000140525 - - 22,0 20,0 0,3,142 0,3,488 0,3,142 0,3,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2829-03B-01W-0728-08,TCGA-AB-2831-03A-01W-0726-08,TCGA-AB-2898-03A-01W-0733-08 99,99,99 AOGC-02-0299,AOGC-02-0530,AOGC-03-0152 99,99,99 chr15:89850944:89850944:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89850944 89850944 A G snp intronic FANCI intronic FANCI intron_variant,NMD_transcript_variant intronic ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE 2.26 0.000786164 ENSG00000140525 - - 22,0 20,0 0,0,145 0,1,490 0,0,145 0,1,486 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0133 99 chr15:89856189:89856189:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89856189 89856189 G A snp nonsynonymous SNV FANCI:NM_001113378:exon35:c.G3706A:p.V1236I,FANCI:NM_018193:exon34:c.G3526A:p.V1176I, nonsynonymous SNV FANCI missense_variant nonsynonymous SNV ENSG00000140525 PASS FALSE TRUE TRUE TRUE TRUE 4.16 0.000784929 ENSG00000140525:ENST00000310775:exon35:c.G3706A:p.V1236I,ENSG00000140525:ENST00000300027:exon34:c.G3526A:p.V1176I, 1002 V/I 21,0 21,0 0,0,146 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0287 99 chr15:89858603:89858603:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89858603 89858603 G A snp nonsynonymous SNV FANCI:NM_001113378:exon37:c.G3907A:p.E1303K,FANCI:NM_018193:exon36:c.G3727A:p.E1243K, nonsynonymous SNV FANCI missense_variant nonsynonymous SNV ENSG00000140525 PASS TRUE TRUE TRUE TRUE TRUE 4.56 0.000787402 ENSG00000140525:ENST00000310775:exon37:c.G3907A:p.E1303K,ENSG00000140525:ENST00000300027:exon36:c.G3727A:p.E1243K, 1069 E/K 59,0 36,0 0,1,144 0,0,490 0,1,144 0,0,481 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2818-03B-01W-0728-08 99 chr15:89858644:89858644:G:C:snp 0.868069852752382 0.0167170549528728 0.10063805270638 0.0125195618153365 0.0125195618153365 1 1 0 chr15 89858644 89858644 G C snp intronic FANCI intronic FANCI regulatory_region_variant intronic - PASS TRUE TRUE TRUE TRUE TRUE 2.71 0.0137457 ENSG00000140525 - - 34,0 8,0 0,4,141 1,10,426 0,4,141 0,4,402 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2803-03B-01W-0728-08,TCGA-AB-2846-03B-01W-0728-08,TCGA-AB-2865-03B-01W-0728-08,TCGA-AB-2918-03A-01W-0745-08 85,99,74,18 AOGC-02-0006,AOGC-02-0013,AOGC-02-0069,AOGC-02-0280,AOGC-02-0301,AOGC-02-0305,AOGC-02-0418,AOGC-02-0476,AOGC-03-0066,AOGC-08-0006,AOGC-08-0051 16,23,15,34,24,6,24,57,26,28,16 chr15:89858692:89858692:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89858692 89858692 C T snp intronic FANCI intronic FANCI regulatory_region_variant intronic - PASS TRUE TRUE TRUE TRUE TRUE 2.09 0.000789889 ENSG00000140525 - - 27,0 8,0 0,1,144 0,0,488 0,1,144 0,0,419 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2837-03B-01W-0728-08 99 chr15:91290633:91290633:T:C:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr15 91290633 91290633 T C snp nonsynonymous SNV BLM:NM_001287247:exon2:c.T11C:p.V4A,BLM:NM_000057:exon2:c.T11C:p.V4A,BLM:NM_001287246:exon3:c.T11C:p.V4A, nonsynonymous SNV BLM missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000197299 PASS FALSE FALSE TRUE TRUE TRUE 5.89 0.00157233 ENSG00000197299:ENST00000560509:exon2:c.T11C:p.V4A,ENSG00000197299:ENST00000559724:exon2:c.T11C:p.V4A,ENSG00000197299:ENST00000355112:exon2:c.T11C:p.V4A, 4 V/A 23,0 8,0 0,0,145 0,2,489 0,0,145 0,1,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0248,AOGC-14-0141 79,99 chr15:91292689:91292689:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91292689 91292689 A T snp nonsynonymous SNV BLM:NM_001287247:exon3:c.A191T:p.D64V,BLM:NM_000057:exon3:c.A191T:p.D64V,BLM:NM_001287246:exon4:c.A191T:p.D64V, nonsynonymous SNV BLM missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000197299 PASS FALSE FALSE TRUE TRUE TRUE 3.46 0.000786164 ENSG00000197299:ENST00000560509:exon3:c.A191T:p.D64V,ENSG00000197299:ENST00000559724:exon3:c.A191T:p.D64V,ENSG00000197299:ENST00000355112:exon3:c.A191T:p.D64V, 64 D/V 22,0 20,0 0,0,145 0,1,490 0,0,145 0,1,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0231 99 chr15:91293061:91293061:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91293061 91293061 A G snp nonsynonymous SNV BLM:NM_001287247:exon3:c.A563G:p.K188R,BLM:NM_000057:exon3:c.A563G:p.K188R,BLM:NM_001287246:exon4:c.A563G:p.K188R, nonsynonymous SNV BLM missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000197299 PASS FALSE TRUE TRUE TRUE TRUE -3.45 0.000786164 ENSG00000197299:ENST00000560509:exon3:c.A563G:p.K188R,ENSG00000197299:ENST00000559724:exon3:c.A563G:p.K188R,ENSG00000197299:ENST00000355112:exon3:c.A563G:p.K188R, 188 K/R 22,0 20,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0091 99 chr15:91293213:91293213:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91293213 91293213 G A snp nonsynonymous SNV BLM:NM_001287247:exon3:c.G715A:p.D239N,BLM:NM_000057:exon3:c.G715A:p.D239N,BLM:NM_001287246:exon4:c.G715A:p.D239N, nonsynonymous SNV BLM missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000197299 PASS FALSE TRUE TRUE TRUE TRUE 3.64 0.000784929 ENSG00000197299:ENST00000560509:exon3:c.G715A:p.D239N,ENSG00000197299:ENST00000559724:exon3:c.G715A:p.D239N,ENSG00000197299:ENST00000355112:exon3:c.G715A:p.D239N, 239 D/N 22,0 20,0 0,0,146 0,1,490 0,0,146 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0319 99 chr15:91295037:91295037:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91295037 91295037 A T snp nonsynonymous SNV BLM:NM_001287247:exon4:c.A820T:p.N274Y,BLM:NM_000057:exon4:c.A820T:p.N274Y,BLM:NM_001287246:exon5:c.A820T:p.N274Y, nonsynonymous SNV BLM missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000197299 PASS FALSE TRUE TRUE TRUE TRUE -2.57 0.000786164 ENSG00000197299:ENST00000560509:exon4:c.A820T:p.N274Y,ENSG00000197299:ENST00000559724:exon4:c.A820T:p.N274Y,ENSG00000197299:ENST00000355112:exon4:c.A820T:p.N274Y, 274 N/Y 31,0 20,0 0,0,146 0,1,489 0,0,145 0,1,464 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0008 99 chr15:91298049:91298049:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91298049 91298049 A G snp nonsynonymous SNV BLM:NM_001287247:exon5:c.A968G:p.K323R,BLM:NM_000057:exon5:c.A968G:p.K323R,BLM:NM_001287246:exon6:c.A968G:p.K323R, nonsynonymous SNV BLM missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000197299 PASS FALSE FALSE TRUE TRUE TRUE 5.24 0.000784929 ENSG00000197299:ENST00000560509:exon5:c.A968G:p.K323R,ENSG00000197299:ENST00000559724:exon5:c.A968G:p.K323R,ENSG00000197299:ENST00000355112:exon5:c.A968G:p.K323R, 323 K/R 22,0 22,0 0,0,146 0,1,490 0,0,145 0,1,478 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0098 99 chr15:91298109:91298109:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91298109 91298109 C G snp stopgain SNV BLM:NM_001287247:exon5:c.C1028G:p.S343X,BLM:NM_000057:exon5:c.C1028G:p.S343X,BLM:NM_001287246:exon6:c.C1028G:p.S343X, stopgain SNV BLM stop_gained,NMD_transcript_variant stopgain SNV ENSG00000197299 PASS FALSE TRUE TRUE TRUE TRUE 4.41 0.000784929 ENSG00000197299:ENST00000560509:exon5:c.C1028G:p.S343X,ENSG00000197299:ENST00000559724:exon5:c.C1028G:p.S343X,ENSG00000197299:ENST00000355112:exon5:c.C1028G:p.S343X, 343 S/* 22,0 22,0 0,0,146 0,1,490 0,0,145 0,1,484 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0059 99 chr15:91303510:91303510:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91303510 91303510 G C snp splicing BLM(NM_001287248:exon6:c.95+1G>C,NM_001287247:exon6:c.1220+1G>C,NM_001287246:exon7:c.1220+1G>C,NM_000057:exon6:c.1220+1G>C) splicing BLM splice_donor_variant,NMD_transcript_variant splicing ENSG00000197299 PASS FALSE TRUE TRUE TRUE TRUE 5.96 0.000793651 ENSG00000197299(ENST00000355112:exon6:c.1220+1G>C,ENST00000560509:exon6:c.1220+1G>C,ENST00000559724:exon6:c.1386+1G>C) - - 20,0 21,0 0,0,145 0,1,484 0,0,145 0,1,439 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0196 99 chr15:91306241:91306241:G:A:snp 0.435974846195726 -0.0997409326424864 0.128035782343122 0.00704225352112676 0.00704225352112676 1 1 0 chr15 91306241 91306241 G A snp nonsynonymous SNV BLM:NM_001287247:exon8:c.G1928A:p.R643H,BLM:NM_001287248:exon8:c.G803A:p.R268H,BLM:NM_000057:exon8:c.G1928A:p.R643H,BLM:NM_001287246:exon9:c.G1928A:p.R643H, nonsynonymous SNV BLM missense_variant nonsynonymous SNV ENSG00000197299 PASS FALSE FALSE FALSE TRUE TRUE -3.93 0.00712025 ENSG00000197299:ENST00000560509:exon8:c.G1928A:p.R643H,ENSG00000197299:ENST00000355112:exon8:c.G1928A:p.R643H, 643 R/H 21,0 22,0 0,1,143 1,6,481 0,1,143 1,4,434 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 0.0170451437460571 1 0 1 TCGA-AB-2880-03A-01W-0732-08 99 AOGC-02-0161,AOGC-02-0247,AOGC-02-0491,AOGC-08-0066,AOGC-08-0255,AOGC-08-0284,AOGC-14-0093 34,51,18,99,99,86,60 chr15:91308637:91308637:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91308637 91308637 C T snp nonsynonymous SNV BLM:NM_001287247:exon9:c.C2186T:p.S729F,BLM:NM_001287248:exon9:c.C1061T:p.S354F,BLM:NM_000057:exon9:c.C2186T:p.S729F,BLM:NM_001287246:exon10:c.C2186T:p.S729F, nonsynonymous SNV BLM missense_variant nonsynonymous SNV ENSG00000197299 PASS FALSE TRUE TRUE TRUE TRUE 5.82 0.000784929 ENSG00000197299:ENST00000560509:exon9:c.C2186T:p.S729F,ENSG00000197299:ENST00000355112:exon9:c.C2186T:p.S729F, 729 S/F 23,0 25,0 0,0,146 0,1,490 0,0,145 0,1,481 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0172 99 chr15:91326134:91326134:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91326134 91326134 G C snp nonsynonymous SNV BLM:NM_001287247:exon13:c.G2638C:p.E880Q,BLM:NM_001287248:exon13:c.G1513C:p.E505Q,BLM:NM_000057:exon13:c.G2638C:p.E880Q,BLM:NM_001287246:exon14:c.G2638C:p.E880Q, nonsynonymous SNV BLM missense_variant nonsynonymous SNV ENSG00000197299 PASS FALSE FALSE TRUE TRUE TRUE 4.56 0.000787402 ENSG00000197299:ENST00000560509:exon13:c.G2638C:p.E880Q,ENSG00000197299:ENST00000355112:exon13:c.G2638C:p.E880Q, 880 E/Q 28,0 22,0 0,0,146 0,1,488 0,0,144 0,1,463 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0304 99 chr15:91328183:91328183:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91328183 91328183 C T snp stopgain SNV BLM:NM_001287247:exon14:c.C2695T:p.R899X,BLM:NM_001287248:exon14:c.C1570T:p.R524X,BLM:NM_000057:exon14:c.C2695T:p.R899X,BLM:NM_001287246:exon15:c.C2695T:p.R899X, stopgain SNV BLM stop_gained stopgain SNV ENSG00000197299 PASS FALSE FALSE TRUE TRUE TRUE 0.359 0.000784929 ENSG00000197299:ENST00000560509:exon14:c.C2695T:p.R899X,ENSG00000197299:ENST00000355112:exon14:c.C2695T:p.R899X, 899 R/* 27,0 21,0 0,0,146 0,1,490 0,0,145 0,1,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-01-0006 99 chr15:91346754:91346754:G:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91346754 91346754 G T snp nonsynonymous SNV BLM:NM_001287248:exon18:c.G2237T:p.S746I,BLM:NM_000057:exon18:c.G3362T:p.S1121I,BLM:NM_001287246:exon19:c.G3362T:p.S1121I, nonsynonymous SNV BLM missense_variant nonsynonymous SNV ENSG00000197299 PASS FALSE FALSE TRUE TRUE TRUE 5.65 0.000789889 ENSG00000197299:ENST00000355112:exon18:c.G3362T:p.S1121I, 1121 S/I 20,0 24,0 0,0,146 0,1,486 0,0,145 0,1,435 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0253 87 chr15:91346808:91346808:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91346808 91346808 G A snp nonsynonymous SNV BLM:NM_001287248:exon18:c.G2291A:p.R764Q,BLM:NM_000057:exon18:c.G3416A:p.R1139Q,BLM:NM_001287246:exon19:c.G3416A:p.R1139Q, nonsynonymous SNV BLM missense_variant nonsynonymous SNV ENSG00000197299 PASS FALSE TRUE TRUE TRUE TRUE 5.65 0.000787402 ENSG00000197299:ENST00000355112:exon18:c.G3416A:p.R1139Q, 1139 R/Q 20,0 24,0 0,0,146 0,1,488 0,0,145 0,1,468 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0104 99 chr15:91346843:91346843:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91346843 91346843 C G snp nonsynonymous SNV BLM:NM_001287248:exon18:c.C2326G:p.L776V,BLM:NM_000057:exon18:c.C3451G:p.L1151V,BLM:NM_001287246:exon19:c.C3451G:p.L1151V, nonsynonymous SNV BLM missense_variant nonsynonymous SNV ENSG00000197299 PASS FALSE TRUE TRUE TRUE TRUE 5.65 0.000787402 ENSG00000197299:ENST00000355112:exon18:c.C3451G:p.L1151V, 1151 L/V 20,0 24,0 0,0,146 0,1,488 0,0,145 0,1,472 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0264 99 chr15:91352464:91352464:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91352464 91352464 G A snp synonymous SNV BLM:NM_001287247:exon18:c.G3456A:p.Q1152Q,BLM:NM_001287248:exon20:c.G2724A:p.Q908Q,BLM:NM_000057:exon20:c.G3849A:p.Q1283Q,BLM:NM_001287246:exon21:c.G3849A:p.Q1283Q, synonymous SNV BLM 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000197299 PASS FALSE FALSE TRUE TRUE TRUE 5.88 0.000788644 ENSG00000197299:ENST00000560509:exon18:c.G3456A:p.Q1152Q,ENSG00000197299:ENST00000355112:exon20:c.G3849A:p.Q1283Q, - - 26,0 22,0 0,0,146 0,1,487 0,0,145 0,1,464 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0023 99 chr15:91354640:91354640:T:G:snp 0.27105525402704 -0.233070866141732 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr15 91354640 91354640 T G snp splicing BLM(NM_001287248:exon21:c.2951+4T>G,NM_001287247:exon19:c.3683+4T>G,NM_001287246:exon22:c.4076+4T>G,NM_000057:exon21:c.4076+4T>G) splicing BLM splice_region_variant,intron_variant,NMD_transcript_variant splicing ENSG00000197299 PASS FALSE FALSE FALSE TRUE TRUE -10.3 0.00316957 ENSG00000197299(ENST00000355112:exon21:c.4076+4T>G,ENST00000560509:exon19:c.3683+4T>G,ENST00000559724:exon21:c.4242+4T>G) - - 29,0 28,0 0,0,146 0,4,481 0,0,145 0,4,414 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0388,AOGC-02-0445,AOGC-08-0063,AOGC-08-0256 99,99,83,99 chr15:91358322:91358322:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91358322 91358322 C T snp intronic BLM intronic BLM intron_variant,NMD_transcript_variant intronic ENSG00000197299 PASS FALSE FALSE FALSE TRUE TRUE 5.76 0.000786164 ENSG00000197299 - - 27,0 21,0 0,1,145 0,0,490 0,1,144 0,0,451 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2869-03A-01W-0761-09 99 chr15:31220711:31220711:-:TGTGTGTGTG:indel:31220709 0.344323526806761 -0.0707338638373115 0.0747986413528051 0.0211267605633803 0.0211267605633803 1 1 0 chr15 31220711 31220711 - TGTGTGTGTG indel:31220709 intronic FAN1 intronic FAN1 non_coding_exon_variant,nc_transcript_variant,feature_elongation intronic ENSG00000198690 PASS TRUE TRUE TRUE TRUE TRUE 0 0.0212264 ENSG00000198690 - - 14,55 61,61 0,4,142 3,17,470 0,4,141 3,11,461 1 0 1 1 0 0 1 0 0 1 0 0 1 1 1 1 0.000209170311750018 1 0 1 TCGA-AB-2840-03D-01W-0755-09,TCGA-AB-2852-03A-01W-0726-08,TCGA-AB-2937-03A-01W-0732-08,TCGA-AB-2948-03A-01W-0755-09 99,99,68,65 AOGC-02-0047,AOGC-02-0130,AOGC-02-0192,AOGC-02-0210,AOGC-02-0269,AOGC-02-0319,AOGC-02-0325,AOGC-02-0400,AOGC-02-0448,AOGC-02-0523,AOGC-03-0033,AOGC-03-0065,AOGC-03-0073,AOGC-03-0116,AOGC-03-0141,AOGC-03-0151,AOGC-08-0006,AOGC-08-0048,AOGC-08-0236,AOGC-14-0156 67,99,31,99,14,74,28,17,20,99,99,17,99,40,82,32,99,76,99,59 chr15:89844495:89844497:TCT:-:indel 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89844495 89844497 TCT - indel intronic FANCI intronic FANCI intron_variant,NMD_transcript_variant,feature_truncation intronic ENSG00000140525 PASS TRUE TRUE TRUE TRUE TRUE 4.01 0.000787402 ENSG00000140525 - - 22,0 21,0 0,1,144 0,0,490 0,1,144 0,0,480 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2837-03B-01W-0728-08 99 chr15:89859676:89859676:-:AAAGG:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 89859676 89859676 - AAAGG indel frameshift insertion FANCI:NM_001113378:exon38:c.3973_3974insAAAGG:p.K1325fs,FANCI:NM_018193:exon37:c.3793_3794insAAAGG:p.K1265fs, frameshift insertion FANCI frameshift_variant,feature_elongation frameshift insertion ENSG00000140525 PASS TRUE TRUE TRUE TRUE TRUE 5.39 0.000786164 ENSG00000140525:ENST00000310775:exon38:c.3973_3974insAAAGG:p.K1325fs,ENSG00000140525:ENST00000300027:exon37:c.3793_3794insAAAGG:p.K1265fs, 1325 - 28,0 21,0 0,0,145 0,1,490 0,0,145 0,1,475 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0443 99 chr15:91295028:91295030:AAG:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91295028 91295030 AAG - indel nonframeshift deletion BLM:NM_001287247:exon4:c.811_813del:p.271_271del,BLM:NM_000057:exon4:c.811_813del:p.271_271del,BLM:NM_001287246:exon5:c.811_813del:p.271_271del, nonframeshift deletion BLM inframe_deletion,NMD_transcript_variant nonframeshift deletion ENSG00000197299 PASS FALSE FALSE TRUE TRUE TRUE 4.65 0.000786164 ENSG00000197299:ENST00000560509:exon4:c.811_813del:p.271_271del,ENSG00000197299:ENST00000559724:exon4:c.811_813del:p.271_271del,ENSG00000197299:ENST00000355112:exon4:c.811_813del:p.271_271del, 271 K/- 31,0 20,0 0,0,146 0,1,489 0,0,145 0,1,459 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-05-0013 99 chr15:91333977:91333977:C:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr15 91333977 91333977 C - indel frameshift deletion BLM:NM_001287247:exon15:c.2922delC:p.Y974fs,BLM:NM_001287248:exon15:c.1797delC:p.Y599fs,BLM:NM_000057:exon15:c.2922delC:p.Y974fs,BLM:NM_001287246:exon16:c.2922delC:p.Y974fs, frameshift deletion BLM frameshift_variant,feature_truncation frameshift deletion ENSG00000197299 PASS TRUE TRUE TRUE TRUE TRUE 3.51 0.000784929 ENSG00000197299:ENST00000560509:exon15:c.2922delC:p.Y974fs,ENSG00000197299:ENST00000355112:exon15:c.2922delC:p.Y974fs, 974 - 22,0 23,0 0,0,146 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0366 99 chr16:3634842:3634842:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3634842 3634842 G C snp nonsynonymous SNV SLX4:NM_032444:exon13:c.C4667G:p.P1556R, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE TRUE TRUE TRUE TRUE 5.47 0.000786164 ENSG00000188827:ENST00000294008:exon13:c.C4667G:p.P1556R, 1556 P/R 26,0 21,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0225 99 chr16:3634861:3634861:G:A:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr16 3634861 3634861 G A snp nonsynonymous SNV SLX4:NM_032444:exon13:c.C4648T:p.R1550W, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE 2.42 0.00235849 ENSG00000188827:ENST00000294008:exon13:c.C4648T:p.R1550W, 1550 R/W 26,0 21,0 0,0,145 0,3,488 0,0,145 0,3,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0207,AOGC-02-0483,AOGC-03-0066 99,99,99 chr16:3639582:3639582:G:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 3639582 3639582 G T snp nonsynonymous SNV SLX4:NM_032444:exon12:c.C4057A:p.H1353N, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE -0.29 0.0017094 ENSG00000188827:ENST00000294008:exon12:c.C4057A:p.H1353N, 1353 H/N 5,0 16,0 0,0,145 0,2,438 0,0,145 0,2,400 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0065,AOGC-02-0069 99,99 chr16:3639689:3639689:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3639689 3639689 G A snp nonsynonymous SNV SLX4:NM_032444:exon12:c.C3950T:p.P1317L, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE TRUE TRUE TRUE TRUE 0.158 0.000840336 ENSG00000188827:ENST00000294008:exon12:c.C3950T:p.P1317L, 1317 P/L 23,0 25,0 0,0,145 0,1,449 0,0,145 0,1,415 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0027 99 chr16:3639782:3639782:G:A:snp 0.704997875659665 -0.0655608214849913 0.173174436921412 0.00469483568075117 0.00469483568075117 1 1 0 chr16 3639782 3639782 G A snp nonsynonymous SNV SLX4:NM_032444:exon12:c.C3857T:p.A1286V, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE FALSE TRUE TRUE -2.33 0.00522648 ENSG00000188827:ENST00000294008:exon12:c.C3857T:p.A1286V, 1286 A/V 21,0 25,0 0,1,144 0,5,424 0,1,144 0,5,395 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2822-03D-01W-0755-09 99 AOGC-02-0006,AOGC-02-0060,AOGC-02-0164,AOGC-02-0226,AOGC-14-0059 99,99,99,99,99 chr16:3640749:3640749:C:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3640749 3640749 C A snp nonsynonymous SNV SLX4:NM_032444:exon12:c.G2890T:p.D964Y, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE -1.25 0.000791139 ENSG00000188827:ENST00000294008:exon12:c.G2890T:p.D964Y, 964 D/Y 20,0 23,0 0,0,145 0,1,486 0,0,145 0,1,445 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0157 99 chr16:3640923:3640923:T:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3640923 3640923 T A snp nonsynonymous SNV SLX4:NM_032444:exon12:c.A2716T:p.M906L, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS TRUE TRUE TRUE TRUE TRUE -5.65 0.000786164 ENSG00000188827:ENST00000294008:exon12:c.A2716T:p.M906L, 906 M/L 22,0 23,0 0,1,144 0,0,491 0,1,144 0,0,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2834-03B-01W-0728-08 99 chr16:3640974:3640974:G:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3640974 3640974 G T snp nonsynonymous SNV SLX4:NM_032444:exon12:c.C2665A:p.Q889K, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE TRUE TRUE TRUE TRUE 0.942 0.000786164 ENSG00000188827:ENST00000294008:exon12:c.C2665A:p.Q889K, 889 Q/K 22,0 13,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0020 99 chr16:3640985:3640985:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3640985 3640985 G A snp nonsynonymous SNV SLX4:NM_032444:exon12:c.C2654T:p.P885L, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE 2.32 0.000786164 ENSG00000188827:ENST00000294008:exon12:c.C2654T:p.P885L, 885 P/L 16,0 13,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0091 99 chr16:3641019:3641019:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3641019 3641019 C T snp nonsynonymous SNV SLX4:NM_032444:exon12:c.G2620A:p.G874S, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE TRUE TRUE TRUE TRUE 2.3 0.000786164 ENSG00000188827:ENST00000294008:exon12:c.G2620A:p.G874S, 874 G/S 9,0 11,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0149 99 chr16:3641060:3641060:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3641060 3641060 G A snp nonsynonymous SNV SLX4:NM_032444:exon12:c.C2579T:p.T860I, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE 5.57 0.000786164 ENSG00000188827:ENST00000294008:exon12:c.C2579T:p.T860I, 860 T/I 20,0 8,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0313 99 chr16:3641202:3641202:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3641202 3641202 C T snp nonsynonymous SNV SLX4:NM_032444:exon12:c.G2437A:p.E813K, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE 5.57 0.000786164 ENSG00000188827:ENST00000294008:exon12:c.G2437A:p.E813K, 813 E/K 20,0 20,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0430 99 chr16:3641280:3641280:C:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 3641280 3641280 C T snp nonsynonymous SNV SLX4:NM_032444:exon12:c.G2359A:p.E787K, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE 1.33 0.00157233 ENSG00000188827:ENST00000294008:exon12:c.G2359A:p.E787K, 787 E/K 20,0 20,0 0,0,145 0,2,489 0,0,145 0,2,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0373,AOGC-08-0097 99,99 chr16:3642722:3642722:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3642722 3642722 C G snp nonsynonymous SNV SLX4:NM_032444:exon11:c.G2305C:p.E769Q, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE 4.64 0.000786164 ENSG00000188827:ENST00000294008:exon11:c.G2305C:p.E769Q, 769 E/Q 8,0 9,0 0,0,145 0,1,490 0,0,140 0,1,481 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0366 94 chr16:3647691:3647691:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3647691 3647691 T C snp nonsynonymous SNV SLX4:NM_032444:exon7:c.A1372G:p.K458E, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE 4.22 0.000788644 ENSG00000188827:ENST00000294008:exon7:c.A1372G:p.K458E, 458 K/E 21,0 5,0 0,0,144 0,1,489 0,0,144 0,1,433 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0062 96 chr16:3651116:3651116:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3651116 3651116 A G snp nonsynonymous SNV SLX4:NM_032444:exon5:c.T1027C:p.F343L, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE TRUE TRUE TRUE TRUE 5.46 0.000786164 ENSG00000188827:ENST00000294008:exon5:c.T1027C:p.F343L, 343 F/L 26,0 22,0 0,0,145 0,1,490 0,0,145 0,1,469 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0380 99 chr16:3651147:3651147:C:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3651147 3651147 C A snp nonsynonymous SNV SLX4:NM_032444:exon5:c.G996T:p.Q332H, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE 1.16 0.000788644 ENSG00000188827:ENST00000294008:exon5:c.G996T:p.Q332H, 332 Q/H 26,0 22,0 0,0,145 0,1,488 0,0,145 0,1,442 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0118 99 chr16:3658881:3658881:G:A:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr16 3658881 3658881 G A snp nonsynonymous SNV SLX4:NM_032444:exon2:c.C85T:p.R29C, nonsynonymous SNV SLX4 missense_variant nonsynonymous SNV ENSG00000188827 PASS FALSE FALSE TRUE TRUE TRUE 1.8 0.00235849 ENSG00000188827:ENST00000294008:exon2:c.C85T:p.R29C, 29 R/C 30,0 25,0 0,0,145 0,3,488 0,0,145 0,3,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0315,AOGC-02-0522,AOGC-08-0170 99,99,99 chr16:11444603:11444603:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 11444603 11444603 A G snp nonsynonymous SNV RMI2:NM_152308:exon2:c.A400G:p.M134V, nonsynonymous SNV RMI2 missense_variant nonsynonymous SNV ENSG00000175643 PASS FALSE TRUE TRUE TRUE TRUE 4.82 0.000786164 ENSG00000175643:ENST00000381820:exon2:c.A211G:p.M71V,ENSG00000175643:ENST00000572173:exon5:c.A211G:p.M71V,ENSG00000175643:ENST00000312499:exon2:c.A400G:p.M134V, 134 M/V 29,0 23,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0119 99 chr16:11444637:11444637:A:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 11444637 11444637 A G snp nonsynonymous SNV RMI2:NM_152308:exon2:c.A434G:p.N145S, nonsynonymous SNV RMI2 missense_variant nonsynonymous SNV ENSG00000175643 PASS FALSE TRUE TRUE TRUE TRUE -6.39 0.000786164 ENSG00000175643:ENST00000381820:exon2:c.A245G:p.N82S,ENSG00000175643:ENST00000572173:exon5:c.A245G:p.N82S,ENSG00000175643:ENST00000312499:exon2:c.A434G:p.N145S, 145 N/S 29,0 23,0 0,1,144 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2849-03B-01W-0728-08 99 chr16:14015897:14015897:A:G:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 14015897 14015897 A G snp nonsynonymous SNV ERCC4:NM_005236:exon2:c.A217G:p.I73V, nonsynonymous SNV ERCC4 missense_variant nonsynonymous SNV ENSG00000175595 PASS FALSE FALSE TRUE TRUE TRUE 5.33 0.00156986 ENSG00000175595:ENST00000575156:exon2:c.A217G:p.I73V,ENSG00000175595:ENST00000311895:exon2:c.A217G:p.I73V, 73 I/V 20,0 21,0 0,1,145 0,1,490 0,1,143 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2846-03B-01W-0728-08 99 AOGC-08-0205 99 chr16:14024708:14024708:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 14024708 14024708 T G snp nonsynonymous SNV ERCC4:NM_005236:exon5:c.T934G:p.S312A, nonsynonymous SNV ERCC4 missense_variant nonsynonymous SNV ENSG00000175595 PASS FALSE TRUE TRUE TRUE TRUE 5.9 0.000788644 ENSG00000175595:ENST00000575156:exon5:c.T934G:p.S312A,ENSG00000175595:ENST00000311895:exon5:c.T934G:p.S312A, 312 S/A 27,0 22,0 0,0,146 0,1,487 0,0,146 0,1,444 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0123 99 chr16:14028081:14028081:C:T:snp 0.946425971912601 -0.00952380952380877 0.141732593760593 0.00704225352112676 0.00704225352112676 1 1 0 chr16 14028081 14028081 C T snp nonsynonymous SNV ERCC4:NM_005236:exon7:c.C1135T:p.P379S, nonsynonymous SNV ERCC4 missense_variant nonsynonymous SNV ENSG00000175595 PASS FALSE FALSE FALSE TRUE TRUE 5.91 0.00706436 ENSG00000175595:ENST00000311895:exon7:c.C1135T:p.P379S, 379 P/S 30,0 22,0 0,2,144 0,7,484 0,2,143 0,7,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2934-03A-01W-0745-08,TCGA-AB-2935-03A-01W-0745-08 99,99 AOGC-03-0008,AOGC-03-0031,AOGC-03-0154,AOGC-05-0017,AOGC-08-0066,AOGC-08-0207,AOGC-08-0301 99,99,81,99,99,99,99 chr16:14029352:14029352:C:G:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 14029352 14029352 C G snp nonsynonymous SNV ERCC4:NM_005236:exon8:c.C1563G:p.S521R, nonsynonymous SNV ERCC4 missense_variant nonsynonymous SNV ENSG00000175595 PASS FALSE FALSE TRUE TRUE TRUE 4.99 0.00157233 ENSG00000175595:ENST00000311895:exon8:c.C1563G:p.S521R, 521 S/R 26,0 27,0 0,0,145 0,2,489 0,0,145 0,2,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0145,AOGC-08-0218 99,99 chr16:14029370:14029370:A:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 14029370 14029370 A T snp nonsynonymous SNV ERCC4:NM_005236:exon8:c.A1581T:p.E527D, nonsynonymous SNV ERCC4 missense_variant nonsynonymous SNV ENSG00000175595 PASS FALSE FALSE TRUE TRUE TRUE -2.51 0.00157233 ENSG00000175595:ENST00000311895:exon8:c.A1581T:p.E527D, 527 E/D 26,0 27,0 0,0,145 0,2,489 0,0,145 0,2,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0340,AOGC-03-0029 99,92 chr16:14031618:14031618:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 14031618 14031618 T C snp splicing ERCC4(NM_005236:exon9:c.1812-5T>C) splicing ERCC4 splice_region_variant,intron_variant splicing ENSG00000175595 PASS FALSE FALSE FALSE TRUE TRUE -0.993 0.000784929 ENSG00000175595(ENST00000311895:exon9:c.1812-5T>C) - - 26,0 21,0 0,1,145 0,0,491 0,1,144 0,0,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2891-03A-01W-0733-08 99 chr16:14041570:14041570:T:C:snp 0.202168134675384 0.270078740157481 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr16 14041570 14041570 T C snp nonsynonymous SNV ERCC4:NM_005236:exon11:c.T2117C:p.I706T, nonsynonymous SNV ERCC4 missense_variant nonsynonymous SNV ENSG00000175595 PASS FALSE FALSE TRUE TRUE TRUE 5.49 0.00314465 ENSG00000175595:ENST00000311895:exon11:c.T2117C:p.I706T, 706 I/T 22,0 21,0 0,2,143 0,2,489 0,2,143 0,2,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2868-03B-01W-0728-08,TCGA-AB-2883-03A-01W-0732-08 99,99 AOGC-02-0064,AOGC-08-0204 99,99 chr16:14041668:14041668:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 14041668 14041668 G A snp nonsynonymous SNV ERCC4:NM_005236:exon11:c.G2215A:p.G739S, nonsynonymous SNV ERCC4 missense_variant nonsynonymous SNV ENSG00000175595 PASS TRUE TRUE TRUE TRUE TRUE 5.79 0.000786164 ENSG00000175595:ENST00000311895:exon11:c.G2215A:p.G739S, 739 G/S 22,0 21,0 0,1,145 0,0,490 0,1,144 0,0,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2861-03B-01W-0728-08 99 chr16:14041719:14041719:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 14041719 14041719 G A snp nonsynonymous SNV ERCC4:NM_005236:exon11:c.G2266A:p.V756M, nonsynonymous SNV ERCC4 missense_variant nonsynonymous SNV ENSG00000175595 PASS FALSE TRUE TRUE TRUE TRUE 0.028 0.000784929 ENSG00000175595:ENST00000311895:exon11:c.G2266A:p.V756M, 756 V/M 22,0 21,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0046 99 chr16:23614913:23614913:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23614913 23614913 A T snp nonsynonymous SNV PALB2:NM_024675:exon13:c.T3428A:p.L1143H, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 5.77 0.000784929 ENSG00000083093:ENST00000261584:exon13:c.T3428A:p.L1143H, 1143 L/H 22,0 20,0 0,0,146 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0215 99 chr16:23619225:23619225:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23619225 23619225 C T snp nonsynonymous SNV PALB2:NM_024675:exon12:c.G3310A:p.G1104S, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 3.08 0.000784929 ENSG00000083093:ENST00000261584:exon12:c.G3310A:p.G1104S, 1104 G/S 27,0 21,0 0,0,146 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0311 99 chr16:23632772:23632772:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23632772 23632772 G A snp synonymous SNV PALB2:NM_024675:exon10:c.C3024T:p.P1008P, synonymous SNV PALB2 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000083093 PASS FALSE FALSE TRUE TRUE TRUE 2.26 0.000786164 ENSG00000083093:ENST00000261584:exon10:c.C3024T:p.P1008P, - - 20,0 21,0 0,0,145 0,1,490 0,0,145 0,1,487 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0036 99 chr16:23635348:23635348:A:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23635348 23635348 A C snp nonsynonymous SNV PALB2:NM_024675:exon8:c.T2816G:p.L939W, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE FALSE TRUE TRUE TRUE 5.81 0.000787402 ENSG00000083093:ENST00000261584:exon8:c.T2816G:p.L939W, 939 L/W 26,0 21,0 0,0,146 0,1,488 0,0,145 0,1,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0126 99 chr16:23635370:23635370:C:T:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr16 23635370 23635370 C T snp nonsynonymous SNV PALB2:NM_024675:exon8:c.G2794A:p.V932M, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE FALSE FALSE TRUE TRUE 4.85 0.00235479 ENSG00000083093:ENST00000261584:exon8:c.G2794A:p.V932M, 932 V/M 26,0 21,0 0,0,146 0,3,488 0,0,145 0,3,484 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0009,AOGC-05-0016,AOGC-08-0190 99,99,99 chr16:23635372:23635372:A:G:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 23635372 23635372 A G snp nonsynonymous SNV PALB2:NM_024675:exon8:c.T2792C:p.L931P, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 5.81 0.00156986 ENSG00000083093:ENST00000261584:exon8:c.T2792C:p.L931P, 931 L/P 26,0 21,0 0,1,145 0,1,490 0,1,144 0,1,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2945-03A-01W-0733-08 99 AOGC-02-0333 99 chr16:23635391:23635391:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23635391 23635391 C G snp nonsynonymous SNV PALB2:NM_024675:exon8:c.G2773C:p.V925L, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 2.73 0.000786164 ENSG00000083093:ENST00000261584:exon8:c.G2773C:p.V925L, 925 V/L 26,0 21,0 0,0,146 0,1,489 0,0,145 0,1,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0132 99 chr16:23637686:23637686:A:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23637686 23637686 A C snp nonsynonymous SNV PALB2:NM_024675:exon7:c.T2619G:p.S873R, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 3.31 0.000784929 ENSG00000083093:ENST00000261584:exon7:c.T2619G:p.S873R, 873 S/R 22,0 23,0 0,0,146 0,1,490 0,0,146 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0124 99 chr16:23637715:23637715:G:A:snp 0.733167316798394 0.0547016274864384 0.160455166401833 0.0054773082942097 0.0054773082942097 1 1 0 chr16 23637715 23637715 G A snp nonsynonymous SNV PALB2:NM_024675:exon7:c.C2590T:p.P864S, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE FALSE FALSE TRUE TRUE 2.82 0.00549451 ENSG00000083093:ENST00000261584:exon7:c.C2590T:p.P864S, 864 P/S 22,0 23,0 0,2,144 0,5,486 0,2,144 0,5,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2863-03B-01W-0728-08,TCGA-AB-2959-03A-01W-0733-08 99,99 AOGC-02-0194,AOGC-02-0467,AOGC-03-0174,AOGC-05-0019,AOGC-08-0194 99,99,99,94,99 chr16:23640599:23640599:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23640599 23640599 G A snp splicing PALB2(NM_024675:exon7:c.2515-3C>T) splicing PALB2 splice_region_variant,intron_variant,NMD_transcript_variant splicing ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 6.17 0.000784929 ENSG00000083093(ENST00000568219:exon7:c.2498-3C>T,ENST00000261584:exon7:c.2515-3C>T,ENST00000565038:exon3:c.87-3C>T) - - 25,0 22,0 0,0,146 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0004 99 chr16:23640635:23640635:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23640635 23640635 T C snp intronic PALB2 intronic PALB2 intron_variant,NMD_transcript_variant intronic ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 3.38 0.000786164 ENSG00000083093 - - 25,0 14,0 0,1,145 0,0,490 0,1,144 0,0,488 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2837-03B-01W-0728-08 99 chr16:23641594:23641594:C:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23641594 23641594 C A snp synonymous SNV PALB2:NM_024675:exon5:c.G1881T:p.V627V, synonymous SNV PALB2 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 5.15 0.000786164 ENSG00000083093:ENST00000261584:exon5:c.G1881T:p.V627V, - - 22,0 23,0 0,0,145 0,1,490 0,0,145 0,1,489 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0258 99 chr16:23646357:23646357:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23646357 23646357 C G snp nonsynonymous SNV PALB2:NM_024675:exon4:c.G1510C:p.V504L, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE FALSE TRUE TRUE TRUE 2.03 0.000786164 ENSG00000083093:ENST00000261584:exon4:c.G1510C:p.V504L, 504 V/L 21,0 21,0 0,0,145 0,1,490 0,0,145 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0478 99 chr16:23646617:23646617:G:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23646617 23646617 G T snp nonsynonymous SNV PALB2:NM_024675:exon4:c.C1250A:p.S417Y, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 5.67 0.000784929 ENSG00000083093:ENST00000261584:exon4:c.C1250A:p.S417Y, 417 S/Y 21,0 21,0 0,0,146 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0340 99 chr16:23646673:23646673:C:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 23646673 23646673 C T snp synonymous SNV PALB2:NM_024675:exon4:c.G1194A:p.V398V, synonymous SNV PALB2 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000083093 PASS FALSE FALSE TRUE TRUE TRUE 2.62 0.00156986 ENSG00000083093:ENST00000261584:exon4:c.G1194A:p.V398V, - - 21,0 21,0 0,0,146 0,2,489 0,0,145 0,1,488 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0358,AOGC-03-0126 58,99 chr16:23646901:23646901:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23646901 23646901 C G snp nonsynonymous SNV PALB2:NM_024675:exon4:c.G966C:p.E322D, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 0.924 0.000784929 ENSG00000083093:ENST00000261584:exon4:c.G966C:p.E322D, 322 E/D 21,0 21,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0065 99 chr16:23647557:23647557:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23647557 23647557 G A snp nonsynonymous SNV PALB2:NM_024675:exon4:c.C310T:p.P104S, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE TRUE TRUE TRUE TRUE 1.38 0.000786164 ENSG00000083093:ENST00000261584:exon4:c.C310T:p.P104S, 104 P/S 21,0 21,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0296 99 chr16:23649405:23649405:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 23649405 23649405 G C snp nonsynonymous SNV PALB2:NM_024675:exon2:c.C94G:p.L32V, nonsynonymous SNV PALB2 missense_variant nonsynonymous SNV ENSG00000083093 PASS FALSE FALSE TRUE TRUE TRUE -1.24 0.000786164 ENSG00000083093:ENST00000561514:exon2:c.C100G:p.L34V,ENSG00000083093:ENST00000261584:exon2:c.C94G:p.L32V,ENSG00000083093:ENST00000568219:exon2:c.C77G:p.T26S, 34 L/V 30,0 25,0 0,0,145 0,1,490 0,0,145 0,1,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0267 99 chr16:89805301:89805301:G:C:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 89805301 89805301 G C snp nonsynonymous SNV FANCA:NM_000135:exon42:c.C4249G:p.H1417D,FANCA:NM_001286167:exon42:c.C4253G:p.T1418R, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE -6.54 0.0015748 ENSG00000187741:ENST00000568369:exon42:c.C4253G:p.T1418R,ENSG00000187741:ENST00000561722:exon4:c.C469G:p.H157D,ENSG00000187741:ENST00000389301:exon42:c.C4249G:p.H1417D,ENSG00000187741:ENST00000567879:exon6:c.C623G:p.T208R, 157 H/D 28,0 22,0 0,1,143 0,1,490 0,1,143 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2897-03A-01W-0733-08 99 AOGC-02-0302 99 chr16:89809336:89809336:G:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89809336 89809336 G C snp nonsynonymous SNV FANCA:NM_000135:exon37:c.C3637G:p.P1213A,FANCA:NM_001286167:exon37:c.C3637G:p.P1213A, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE -4.8 0.000786164 ENSG00000187741:ENST00000568369:exon37:c.C3637G:p.P1213A,ENSG00000187741:ENST00000389301:exon37:c.C3637G:p.P1213A,ENSG00000187741:ENST00000567879:exon2:c.C115G:p.P39A, 1213 P/A 26,0 21,0 0,1,144 0,0,491 0,1,144 0,0,479 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2879-03A-01W-0732-08 99 chr16:89813075:89813075:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89813075 89813075 G A snp nonsynonymous SNV FANCA:NM_000135:exon35:c.C3430T:p.R1144W,FANCA:NM_001286167:exon35:c.C3430T:p.R1144W, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE 3.2 0.000784929 ENSG00000187741:ENST00000568369:exon35:c.C3430T:p.R1144W,ENSG00000187741:ENST00000389301:exon35:c.C3430T:p.R1144W, 1144 R/W 21,0 10,0 0,1,145 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2870-03A-01W-0732-08 99 chr16:89813078:89813078:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89813078 89813078 G C snp nonsynonymous SNV FANCA:NM_000135:exon35:c.C3427G:p.L1143V,FANCA:NM_001286167:exon35:c.C3427G:p.L1143V, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE TRUE TRUE TRUE TRUE -10.8 0.000784929 ENSG00000187741:ENST00000568369:exon35:c.C3427G:p.L1143V,ENSG00000187741:ENST00000389301:exon35:c.C3427G:p.L1143V, 1143 L/V 21,0 10,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0258 99 chr16:89813093:89813093:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89813093 89813093 G C snp nonsynonymous SNV FANCA:NM_000135:exon35:c.C3412G:p.L1138V,FANCA:NM_001286167:exon35:c.C3412G:p.L1138V, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE TRUE TRUE TRUE TRUE 5.39 0.000784929 ENSG00000187741:ENST00000568369:exon35:c.C3412G:p.L1138V,ENSG00000187741:ENST00000389301:exon35:c.C3412G:p.L1138V, 1138 L/V 21,0 10,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0397 99 chr16:89816278:89816278:G:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 89816278 89816278 G T snp nonsynonymous SNV FANCA:NM_000135:exon32:c.C3099A:p.D1033E,FANCA:NM_001286167:exon32:c.C3099A:p.D1033E, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE -0.479 0.00157233 ENSG00000187741:ENST00000568369:exon32:c.C3099A:p.D1033E,ENSG00000187741:ENST00000389301:exon32:c.C3099A:p.D1033E, 1033 D/E 29,0 21,0 0,0,145 0,2,489 0,0,145 0,2,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0165,AOGC-02-0202 99,99 chr16:89818556:89818556:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89818556 89818556 G C snp nonsynonymous SNV FANCA:NM_000135:exon31:c.C3056G:p.S1019C,FANCA:NM_001286167:exon31:c.C3056G:p.S1019C, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE TRUE TRUE TRUE TRUE 3.14 0.000786164 ENSG00000187741:ENST00000568369:exon31:c.C3056G:p.S1019C,ENSG00000187741:ENST00000389301:exon31:c.C3056G:p.S1019C, 1019 S/C 29,0 22,0 0,0,145 0,1,490 0,0,145 0,1,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0284 99 chr16:89818580:89818580:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89818580 89818580 C T snp nonsynonymous SNV FANCA:NM_000135:exon31:c.G3032A:p.R1011H,FANCA:NM_001286167:exon31:c.G3032A:p.R1011H, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE TRUE TRUE TRUE TRUE -4.86 0.000784929 ENSG00000187741:ENST00000568369:exon31:c.G3032A:p.R1011H,ENSG00000187741:ENST00000389301:exon31:c.G3032A:p.R1011H, 1011 R/H 29,0 22,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0144 99 chr16:89831288:89831288:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89831288 89831288 G A snp intronic FANCA unknown FANCA missense_variant,NMD_transcript_variant intronic ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE -3.16 0.000786164 UNKNOWN 24 R/C 22,0 21,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0035 99 chr16:89831418:89831418:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89831418 89831418 C G snp nonsynonymous SNV FANCA:NM_000135:exon28:c.G2658C:p.E886D,FANCA:NM_001286167:exon28:c.G2658C:p.E886D, nonsynonymous SNV FANCA missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000187741 PASS FALSE TRUE TRUE TRUE TRUE -3.23 0.000784929 ENSG00000187741:ENST00000568369:exon28:c.G2658C:p.E886D,ENSG00000187741:ENST00000389301:exon28:c.G2658C:p.E886D, 22 E/D 22,0 21,0 0,0,146 0,1,490 0,0,146 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0147 99 chr16:89836359:89836359:G:A:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 89836359 89836359 G A snp nonsynonymous SNV FANCA:NM_000135:exon26:c.C2390T:p.A797V,FANCA:NM_001286167:exon26:c.C2390T:p.A797V, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE -9.26 0.0015949 ENSG00000187741:ENST00000568369:exon26:c.C2390T:p.A797V,ENSG00000187741:ENST00000389301:exon26:c.C2390T:p.A797V,ENSG00000187741:ENST00000567205:exon1:c.C74T:p.A25V, 797 A/V 5,0 7,0 0,1,143 0,1,482 0,1,142 0,1,457 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2894-03A-01W-0733-08 99 AOGC-08-0158 99 chr16:89836978:89836978:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89836978 89836978 G A snp nonsynonymous SNV FANCA:NM_000135:exon24:c.C2216T:p.P739L,FANCA:NM_001286167:exon24:c.C2216T:p.P739L, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE FALSE TRUE TRUE 4.9 0.000818331 ENSG00000187741:ENST00000568369:exon24:c.C2216T:p.P739L,ENSG00000187741:ENST00000389301:exon24:c.C2216T:p.P739L, 739 P/L 3,0 6,0 0,1,140 0,0,470 0,1,120 0,0,410 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2901-03A-01W-0733-08 99 chr16:89838178:89838178:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89838178 89838178 C T snp nonsynonymous SNV FANCA:NM_000135:exon23:c.G2059A:p.V687I,FANCA:NM_001286167:exon23:c.G2059A:p.V687I, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE TRUE TRUE TRUE TRUE 1.4 0.000787402 ENSG00000187741:ENST00000568369:exon23:c.G2059A:p.V687I,ENSG00000187741:ENST00000389301:exon23:c.G2059A:p.V687I, 687 V/I 29,0 28,0 0,0,145 0,1,489 0,0,145 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0008 99 chr16:89842176:89842176:C:G:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 89842176 89842176 C G snp nonsynonymous SNV FANCA:NM_000135:exon21:c.G1874C:p.C625S,FANCA:NM_001286167:exon21:c.G1874C:p.C625S, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE 5.03 0.00156986 ENSG00000187741:ENST00000568369:exon21:c.G1874C:p.C625S,ENSG00000187741:ENST00000389301:exon21:c.G1874C:p.C625S, 625 C/S 12,0 9,0 0,0,146 0,2,489 0,0,141 0,2,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0031,AOGC-02-0283 99,99 chr16:89857830:89857830:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89857830 89857830 G A snp nonsynonymous SNV FANCA:NM_000135:exon14:c.C1340T:p.S447L,FANCA:NM_001286167:exon14:c.C1340T:p.S447L, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE 5.43 0.000789889 ENSG00000187741:ENST00000568369:exon14:c.C1340T:p.S447L,ENSG00000187741:ENST00000389301:exon14:c.C1340T:p.S447L, 447 S/L 28,0 15,0 0,0,145 0,1,487 0,0,145 0,1,459 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0167 99 chr16:89858410:89858410:C:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 89858410 89858410 C A snp nonsynonymous SNV FANCA:NM_000135:exon13:c.G1150T:p.V384F,FANCA:NM_001286167:exon13:c.G1150T:p.V384F, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE 5.49 0.00156986 ENSG00000187741:ENST00000568369:exon13:c.G1150T:p.V384F,ENSG00000187741:ENST00000389301:exon13:c.G1150T:p.V384F, 384 V/F 25,0 23,0 0,0,146 0,2,489 0,0,145 0,2,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0046,AOGC-03-0124 99,99 chr16:89862376:89862376:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89862376 89862376 G C snp nonsynonymous SNV FANCA:NM_000135:exon11:c.C944G:p.P315R,FANCA:NM_001286167:exon11:c.C944G:p.P315R, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE TRUE TRUE TRUE TRUE 3.31 0.000784929 ENSG00000187741:ENST00000568369:exon11:c.C944G:p.P315R,ENSG00000187741:ENST00000389301:exon11:c.C944G:p.P315R, 315 P/R 28,0 22,0 0,0,146 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0267 99 chr16:89865359:89865359:C:G:snp 0.675730396862748 0.102201257861636 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr16 89865359 89865359 C G snp UTR3 FANCA UTR3 FANCA splice_region_variant,3_prime_UTR_variant,NMD_transcript_variant UTR3 ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE -1.48 0.0023622 ENSG00000187741 - - 22,0 22,0 0,1,144 0,2,488 0,1,144 0,2,472 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2944-03A-01W-0755-09 99 AOGC-02-0243,AOGC-08-0066 99,99 chr16:89865516:89865516:T:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr16 89865516 89865516 T A snp intronic FANCA stoploss SNV FANCA stop_lost intronic ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE -4.24 0.00157233 ENSG00000187741:ENST00000563673:exon10:c.A951T:p.X317Y, 317 */Y 22,0 22,0 0,0,145 0,2,489 0,0,145 0,2,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0001,AOGC-08-0267 99,99 chr16:89865521:89865521:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89865521 89865521 T G snp intronic FANCA nonsynonymous SNV FANCA missense_variant intronic ENSG00000187741 PASS FALSE TRUE TRUE TRUE TRUE -4.34 0.000786164 ENSG00000187741:ENST00000563673:exon10:c.A946C:p.N316H, 316 N/H 22,0 22,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0143 99 chr16:89865593:89865593:G:C:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr16 89865593 89865593 G C snp nonsynonymous SNV FANCA:NM_001018112:exon10:c.C874G:p.H292D,FANCA:NM_000135:exon10:c.C874G:p.H292D,FANCA:NM_001286167:exon10:c.C874G:p.H292D, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE -2.43 0.00235479 ENSG00000187741:ENST00000568369:exon10:c.C874G:p.H292D,ENSG00000187741:ENST00000563673:exon10:c.C874G:p.H292D,ENSG00000187741:ENST00000389301:exon10:c.C874G:p.H292D,ENSG00000187741:ENST00000543736:exon9:c.C778G:p.H260D,ENSG00000187741:ENST00000534992:exon10:c.C874G:p.H292D,ENSG00000187741:ENST00000389302:exon10:c.C874G:p.H292D, 292 H/D 22,0 22,0 0,0,146 0,3,488 0,0,145 0,3,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0136,AOGC-02-0523,AOGC-03-0062 99,99,99 chr16:89865610:89865610:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89865610 89865610 T C snp nonsynonymous SNV FANCA:NM_001018112:exon10:c.A857G:p.Q286R,FANCA:NM_000135:exon10:c.A857G:p.Q286R,FANCA:NM_001286167:exon10:c.A857G:p.Q286R, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE FALSE TRUE TRUE 2.35 0.000784929 ENSG00000187741:ENST00000568369:exon10:c.A857G:p.Q286R,ENSG00000187741:ENST00000563673:exon10:c.A857G:p.Q286R,ENSG00000187741:ENST00000389301:exon10:c.A857G:p.Q286R,ENSG00000187741:ENST00000543736:exon9:c.A761G:p.Q254R,ENSG00000187741:ENST00000534992:exon10:c.A857G:p.Q286R,ENSG00000187741:ENST00000389302:exon10:c.A857G:p.Q286R, 286 Q/R 22,0 22,0 0,1,145 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2850-03B-01W-0728-08 99 chr16:89880993:89880993:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89880993 89880993 G A snp nonsynonymous SNV FANCA:NM_001018112:exon3:c.C218T:p.S73F,FANCA:NM_000135:exon3:c.C218T:p.S73F,FANCA:NM_001286167:exon3:c.C218T:p.S73F, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE TRUE TRUE TRUE TRUE 3.98 0.000787402 ENSG00000187741:ENST00000568369:exon3:c.C218T:p.S73F,ENSG00000187741:ENST00000565582:exon2:c.C131T:p.S44F,ENSG00000187741:ENST00000563673:exon3:c.C218T:p.S73F,ENSG00000187741:ENST00000563513:exon3:c.C218T:p.S73F,ENSG00000187741:ENST00000389301:exon3:c.C218T:p.S73F,ENSG00000187741:ENST00000543736:exon3:c.C218T:p.S73F,ENSG00000187741:ENST00000534992:exon3:c.C218T:p.S73F,ENSG00000187741:ENST00000389302:exon3:c.C218T:p.S73F, 73 S/F 21,0 20,0 0,0,145 0,1,489 0,0,145 0,1,474 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0244 99 chr16:89881011:89881011:G:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 89881011 89881011 G T snp nonsynonymous SNV FANCA:NM_001018112:exon3:c.C200A:p.P67Q,FANCA:NM_000135:exon3:c.C200A:p.P67Q,FANCA:NM_001286167:exon3:c.C200A:p.P67Q, nonsynonymous SNV FANCA missense_variant nonsynonymous SNV ENSG00000187741 PASS FALSE FALSE TRUE TRUE TRUE 1.8 0.000786164 ENSG00000187741:ENST00000568369:exon3:c.C200A:p.P67Q,ENSG00000187741:ENST00000565582:exon2:c.C113A:p.P38Q,ENSG00000187741:ENST00000563673:exon3:c.C200A:p.P67Q,ENSG00000187741:ENST00000563513:exon3:c.C200A:p.P67Q,ENSG00000187741:ENST00000389301:exon3:c.C200A:p.P67Q,ENSG00000187741:ENST00000543736:exon3:c.C200A:p.P67Q,ENSG00000187741:ENST00000534992:exon3:c.C200A:p.P67Q,ENSG00000187741:ENST00000389302:exon3:c.C200A:p.P67Q, 67 P/Q 21,0 20,0 0,0,146 0,1,489 0,0,145 0,1,472 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0483 99 chr16:3633101:3633102:TG:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3633101 3633102 TG - indel frameshift deletion SLX4:NM_032444:exon14:c.5149_5150del:p.1717_1717del, frameshift deletion SLX4 frameshift_variant,feature_truncation frameshift deletion ENSG00000188827 PASS TRUE TRUE TRUE TRUE TRUE 5.28 0.000794913 ENSG00000188827:ENST00000294008:exon14:c.5149_5150del:p.1717_1717del, 1717 - 21,0 22,0 0,0,145 0,1,483 0,0,144 0,1,423 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0208 99 chr16:3634840:3634840:-:G:indel 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3634840 3634840 - G indel frameshift insertion SLX4:NM_032444:exon13:c.4669_4670insC:p.K1557fs, frameshift insertion SLX4 frameshift_variant,feature_elongation frameshift insertion ENSG00000188827 PASS TRUE TRUE TRUE TRUE TRUE 5.47 0.000786164 ENSG00000188827:ENST00000294008:exon13:c.4669_4670insC:p.K1557fs, 1556-1557 - 26,0 21,0 0,1,144 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2863-03B-01W-0728-08 99 chr16:3640054:3640056:AAT:-:indel 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 3640054 3640056 AAT - indel nonframeshift deletion SLX4:NM_032444:exon12:c.3583_3585del:p.1195_1195del, nonframeshift deletion SLX4 inframe_deletion nonframeshift deletion ENSG00000188827 PASS FALSE TRUE TRUE TRUE TRUE 5.86 0.000786164 ENSG00000188827:ENST00000294008:exon12:c.3583_3585del:p.1195_1195del, 1195 I/- 21,0 23,0 0,1,144 0,0,491 0,1,144 0,0,484 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2818-03B-01W-0728-08 99 chr16:14027998:14027999:TT:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr16 14027998 14027999 TT - indel intronic ERCC4 ncRNA_exonic ERCC4 non_coding_exon_variant,nc_transcript_variant,feature_truncation intronic ENSG00000262732 PASS TRUE TRUE TRUE TRUE TRUE 2.97 0.000792393 ENSG00000262732 - - 8,0 2,0 0,0,143 0,1,487 0,0,128 0,1,450 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0205 99 chr16:89816087:89816105:TGCTGCCCTGCCCAGGTGG:-:indel 0.0736113257430485 0.437106918238994 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr16 89816087 89816105 TGCTGCCCTGCCCAGGTGG - indel intronic FANCA intronic FANCA regulatory_region_variant intronic - PASS FALSE FALSE TRUE TRUE TRUE 0 0.00237342 ENSG00000187741 - - 7,0 2,0 0,2,141 0,1,488 0,2,131 0,1,454 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2803-03B-01W-0728-08,TCGA-AB-2874-03A-01W-0732-08 99,99 AOGC-08-0025 99 chr17:1747133:1747133:C:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1747133 1747133 C A snp intronic RPA1 intronic RPA1 intron_variant intronic ENSG00000132383 PASS FALSE FALSE TRUE TRUE TRUE 2.3 0.000786164 ENSG00000132383 - - 21,0 2,0 0,0,145 0,1,490 0,0,144 0,1,450 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0373 99 chr17:1747844:1747844:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1747844 1747844 A T snp intronic RPA1 intronic RPA1 intron_variant intronic ENSG00000132383 PASS FALSE FALSE TRUE TRUE TRUE 3.33 0.000786164 ENSG00000132383 - - 22,0 7,0 0,0,145 0,1,490 0,0,145 0,1,487 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0113 99 chr17:1747909:1747909:G:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1747909 1747909 G C snp nonsynonymous SNV RPA1:NM_002945:exon4:c.G201C:p.E67D, nonsynonymous SNV RPA1 missense_variant nonsynonymous SNV ENSG00000132383 PASS TRUE TRUE TRUE TRUE TRUE -2.11 0.000786164 ENSG00000132383:ENST00000254719:exon4:c.G201C:p.E67D,ENSG00000132383:ENST00000570451:exon4:c.G162C:p.E54D,ENSG00000132383:ENST00000571058:exon4:c.G162C:p.E54D, 67 E/D 22,0 22,0 0,1,144 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2955-03A-01W-0733-08 99 chr17:1748046:1748046:G:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr17 1748046 1748046 G A snp intronic RPA1 intronic RPA1 intron_variant intronic ENSG00000132383 PASS FALSE FALSE TRUE TRUE TRUE 3.63 0.00158479 ENSG00000132383 - - 10,0 3,0 0,0,143 0,2,486 0,0,129 0,2,451 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-01-0003,AOGC-02-0064 99,99 chr17:1782558:1782558:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1782558 1782558 C T snp nonsynonymous SNV RPA1:NM_002945:exon10:c.C809T:p.T270I, nonsynonymous SNV RPA1 missense_variant nonsynonymous SNV ENSG00000132383 PASS FALSE TRUE TRUE TRUE TRUE 6.08 0.000784929 ENSG00000132383:ENST00000254719:exon10:c.C809T:p.T270I,ENSG00000132383:ENST00000574049:exon2:c.C77T:p.T26I, 270 T/I 20,0 21,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0380 99 chr17:1782605:1782605:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1782605 1782605 G A snp nonsynonymous SNV RPA1:NM_002945:exon10:c.G856A:p.V286I, nonsynonymous SNV RPA1 missense_variant nonsynonymous SNV ENSG00000132383 PASS FALSE TRUE TRUE TRUE TRUE 6.08 0.000784929 ENSG00000132383:ENST00000254719:exon10:c.G856A:p.V286I,ENSG00000132383:ENST00000574049:exon2:c.G124A:p.V42I, 286 V/I 20,0 21,0 0,0,146 0,1,490 0,0,146 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0180 99 chr17:1782669:1782669:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1782669 1782669 A G snp nonsynonymous SNV RPA1:NM_002945:exon10:c.A920G:p.D307G, nonsynonymous SNV RPA1 missense_variant nonsynonymous SNV ENSG00000132383 PASS FALSE TRUE TRUE TRUE TRUE 5 0.000784929 ENSG00000132383:ENST00000254719:exon10:c.A920G:p.D307G,ENSG00000132383:ENST00000574049:exon2:c.A188G:p.D63G, 307 D/G 20,0 21,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0425 99 chr17:1783970:1783970:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1783970 1783970 A T snp nonsynonymous SNV RPA1:NM_002945:exon12:c.A1226T:p.Y409F, nonsynonymous SNV RPA1 missense_variant nonsynonymous SNV ENSG00000132383 PASS FALSE TRUE TRUE TRUE TRUE 4.98 0.000786164 ENSG00000132383:ENST00000254719:exon12:c.A1226T:p.Y409F,ENSG00000132383:ENST00000574049:exon4:c.A494T:p.Y165F, 409 Y/F 20,0 29,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0156 99 chr17:1784021:1784021:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1784021 1784021 G A snp intronic RPA1 intronic RPA1 intron_variant intronic ENSG00000132383 PASS FALSE TRUE TRUE TRUE TRUE 2.42 0.000786164 ENSG00000132383 - - 20,0 29,0 0,0,145 0,1,490 0,0,145 0,1,485 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0317 99 chr17:1784066:1784066:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1784066 1784066 C T snp intronic RPA1 intronic RPA1 intron_variant intronic ENSG00000132383 PASS TRUE TRUE TRUE TRUE TRUE 2.67 0.000786164 ENSG00000132383 - - 20,0 8,0 0,1,144 0,0,491 0,1,144 0,0,468 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2818-03B-01W-0728-08 99 chr17:1787078:1787078:C:T:snp 0.930368235661057 0.0185039370078748 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr17 1787078 1787078 C T snp intronic RPA1 intronic RPA1 intron_variant intronic ENSG00000132383 PASS FALSE FALSE TRUE TRUE TRUE 2.37 0.00314465 ENSG00000132383 - - 22,0 21,0 0,1,144 0,3,488 0,1,144 0,2,486 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2850-03B-01W-0728-08 99 AOGC-02-0418,AOGC-02-0513,AOGC-03-0118 99,56,99 chr17:1791991:1791991:C:G:snp 0.866515946988662 -0.0318611987381696 0.189553423814011 0.00391236306729264 0.00391236306729264 1 1 0 chr17 1791991 1791991 C G snp nonsynonymous SNV RPA1:NM_002945:exon14:c.C1397G:p.A466G, nonsynonymous SNV RPA1 missense_variant nonsynonymous SNV ENSG00000132383 PASS FALSE FALSE TRUE TRUE TRUE 4.03 0.00392465 ENSG00000132383:ENST00000254719:exon14:c.C1397G:p.A466G, 466 A/G 26,0 23,0 0,1,145 0,4,487 0,1,144 0,4,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2853-03D-01W-0755-09 99 AOGC-02-0535,AOGC-08-0154,AOGC-08-0218,AOGC-08-0283 99,52,99,99 chr17:1792132:1792132:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1792132 1792132 G A snp nonsynonymous SNV RPA1:NM_002945:exon14:c.G1538A:p.R513H, nonsynonymous SNV RPA1 missense_variant nonsynonymous SNV ENSG00000132383 PASS FALSE FALSE TRUE TRUE TRUE 6.14 0.000784929 ENSG00000132383:ENST00000254719:exon14:c.G1538A:p.R513H, 513 R/H 26,0 23,0 0,0,146 0,1,490 0,0,146 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0158 99 chr17:1795142:1795142:T:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1795142 1795142 T A snp nonsynonymous SNV RPA1:NM_002945:exon15:c.T1567A:p.F523I, nonsynonymous SNV RPA1 missense_variant nonsynonymous SNV ENSG00000132383 PASS FALSE TRUE TRUE TRUE TRUE 5.72 0.000784929 ENSG00000132383:ENST00000254719:exon15:c.T1567A:p.F523I,ENSG00000132383:ENST00000574049:exon6:c.T658A:p.F220I, 523 F/I 20,0 24,0 0,0,146 0,1,490 0,0,145 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0082 99 chr17:1798389:1798389:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 1798389 1798389 C T snp synonymous SNV RPA1:NM_002945:exon16:c.C1746T:p.N582N, synonymous SNV RPA1 splice_region_variant,synonymous_variant synonymous SNV ENSG00000132383 PASS FALSE FALSE TRUE TRUE TRUE -1.99 0.000787402 ENSG00000132383:ENST00000254719:exon16:c.C1746T:p.N582N,ENSG00000132383:ENST00000574049:exon7:c.C837T:p.N279N, 582 N 26,0 20,0 0,0,145 0,1,489 0,0,145 0,1,474 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0340 99 chr17:18181205:18181205:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 18181205 18181205 G C snp nonsynonymous SNV TOP3A:NM_004618:exon18:c.C2611G:p.L871V, nonsynonymous SNV TOP3A missense_variant nonsynonymous SNV ENSG00000177302 PASS FALSE TRUE TRUE TRUE TRUE 1.97 0.000814332 ENSG00000177302:ENST00000542570:exon17:c.C2326G:p.L776V,ENSG00000177302:ENST00000321105:exon18:c.C2611G:p.L871V,ENSG00000177302:ENST00000540524:exon9:c.C1201G:p.L401V,ENSG00000177302:ENST00000580095:exon18:c.C2536G:p.L846V, 846 L/V 10,0 8,0 0,0,145 0,1,468 0,0,144 0,1,416 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0333 99 chr17:18181546:18181546:G:A:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr17 18181546 18181546 G A snp nonsynonymous SNV TOP3A:NM_004618:exon18:c.C2270T:p.P757L, nonsynonymous SNV TOP3A missense_variant nonsynonymous SNV ENSG00000177302 PASS FALSE FALSE TRUE TRUE TRUE 3.55 0.00236967 ENSG00000177302:ENST00000542570:exon17:c.C1985T:p.P662L,ENSG00000177302:ENST00000321105:exon18:c.C2270T:p.P757L,ENSG00000177302:ENST00000540524:exon9:c.C860T:p.P287L,ENSG00000177302:ENST00000580095:exon18:c.C2195T:p.P732L, 732 P/L 15,0 11,0 0,0,145 0,3,485 0,0,145 0,3,417 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0169,AOGC-08-0285,AOGC-14-0081 99,30,67 chr17:18181600:18181600:C:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 18181600 18181600 C A snp nonsynonymous SNV TOP3A:NM_004618:exon18:c.G2216T:p.G739V, nonsynonymous SNV TOP3A missense_variant nonsynonymous SNV ENSG00000177302 PASS FALSE TRUE TRUE TRUE TRUE 5.72 0.000792393 ENSG00000177302:ENST00000542570:exon17:c.G1931T:p.G644V,ENSG00000177302:ENST00000321105:exon18:c.G2216T:p.G739V,ENSG00000177302:ENST00000540524:exon9:c.G806T:p.G269V,ENSG00000177302:ENST00000580095:exon18:c.G2141T:p.G714V, 714 G/V 22,0 22,0 0,1,144 0,0,486 0,1,144 0,0,447 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2805-03B-01W-0728-08 99 chr17:18181601:18181601:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 18181601 18181601 C T snp nonsynonymous SNV TOP3A:NM_004618:exon18:c.G2215A:p.G739R, nonsynonymous SNV TOP3A missense_variant nonsynonymous SNV ENSG00000177302 PASS FALSE FALSE TRUE TRUE TRUE 5.72 0.000792393 ENSG00000177302:ENST00000542570:exon17:c.G1930A:p.G644R,ENSG00000177302:ENST00000321105:exon18:c.G2215A:p.G739R,ENSG00000177302:ENST00000540524:exon9:c.G805A:p.G269R,ENSG00000177302:ENST00000580095:exon18:c.G2140A:p.G714R, 714 G/R 22,0 22,0 0,0,145 0,1,485 0,0,145 0,1,448 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0441 99 chr17:18186148:18186148:C:T:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr17 18186148 18186148 C T snp nonsynonymous SNV TOP3A:NM_004618:exon16:c.G1885A:p.E629K, nonsynonymous SNV TOP3A missense_variant nonsynonymous SNV ENSG00000177302 PASS FALSE FALSE TRUE TRUE TRUE 4.69 0.00237342 ENSG00000177302:ENST00000542570:exon15:c.G1600A:p.E534K,ENSG00000177302:ENST00000321105:exon16:c.G1885A:p.E629K,ENSG00000177302:ENST00000540524:exon7:c.G475A:p.E159K,ENSG00000177302:ENST00000580095:exon16:c.G1810A:p.E604K, 604 E/K 24,0 23,0 0,0,145 0,3,484 0,0,145 0,3,453 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0016,AOGC-03-0014,AOGC-14-0141 99,99,99 chr17:18188582:18188582:A:C:snp 0.811375565860404 -0.0321144674085843 0.134566185463994 0.00782472613458529 0.00782472613458529 1 1 0 chr17 18188582 18188582 A C snp nonsynonymous SNV TOP3A:NM_004618:exon15:c.T1751G:p.L584R, nonsynonymous SNV TOP3A missense_variant nonsynonymous SNV ENSG00000177302 PASS FALSE FALSE FALSE TRUE TRUE 5.4 0.00786164 ENSG00000177302:ENST00000542570:exon14:c.T1466G:p.L489R,ENSG00000177302:ENST00000321105:exon15:c.T1751G:p.L584R,ENSG00000177302:ENST00000582122:exon4:c.T376G:p.S126A,ENSG00000177302:ENST00000540524:exon6:c.T341G:p.L114R,ENSG00000177302:ENST00000580095:exon15:c.T1676G:p.L559R, 559 L/R 29,0 7,0 0,2,143 0,8,483 0,2,143 0,8,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2919-03A-01W-0745-08,TCGA-AB-2957-03A-01W-0733-08 99,99 AOGC-02-0026,AOGC-02-0125,AOGC-02-0171,AOGC-02-0413,AOGC-02-0533,AOGC-03-0157,AOGC-08-0186,AOGC-08-0301 99,99,99,99,99,99,99,99 chr17:18193987:18193987:T:C:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr17 18193987 18193987 T C snp nonsynonymous SNV TOP3A:NM_004618:exon13:c.A1481G:p.Y494C, nonsynonymous SNV TOP3A missense_variant nonsynonymous SNV ENSG00000177302 PASS FALSE FALSE TRUE TRUE TRUE 5.66 0.00235849 ENSG00000177302:ENST00000542570:exon12:c.A1196G:p.Y399C,ENSG00000177302:ENST00000321105:exon13:c.A1481G:p.Y494C,ENSG00000177302:ENST00000582122:exon2:c.A89G:p.Y30C,ENSG00000177302:ENST00000540524:exon4:c.A71G:p.Y24C,ENSG00000177302:ENST00000580095:exon13:c.A1406G:p.Y469C, 469 Y/C 50,0 17,0 0,0,145 0,3,488 0,0,144 0,3,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0063,AOGC-08-0167,AOGC-08-0170 99,99,99 chr17:18198068:18198068:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 18198068 18198068 C T snp nonsynonymous SNV TOP3A:NM_004618:exon10:c.G1022A:p.R341K, nonsynonymous SNV TOP3A missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000177302 PASS FALSE FALSE TRUE TRUE TRUE 0.446 0.000786164 ENSG00000177302:ENST00000542570:exon9:c.G737A:p.R246K,ENSG00000177302:ENST00000321105:exon10:c.G1022A:p.R341K,ENSG00000177302:ENST00000580095:exon10:c.G947A:p.R316K, 103 R/K 27,0 13,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0427 99 chr17:18205933:18205933:C:T:snp 0.0736113257430485 0.437106918238994 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr17 18205933 18205933 C T snp nonsynonymous SNV TOP3A:NM_004618:exon6:c.G604A:p.D202N, nonsynonymous SNV TOP3A missense_variant nonsynonymous SNV ENSG00000177302 PASS FALSE FALSE TRUE TRUE TRUE 5.1 0.00235479 ENSG00000177302:ENST00000542570:exon5:c.G319A:p.D107N,ENSG00000177302:ENST00000321105:exon6:c.G604A:p.D202N,ENSG00000177302:ENST00000580095:exon6:c.G529A:p.D177N, 177 D/N 34,0 22,0 0,2,144 0,1,490 0,2,143 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2837-03B-01W-0728-08,TCGA-AB-2889-03A-01W-0732-08 99,99 AOGC-02-0174 99 chr17:18208533:18208533:T:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 18208533 18208533 T A snp nonsynonymous SNV TOP3A:NM_004618:exon5:c.A392T:p.K131I, nonsynonymous SNV TOP3A missense_variant,splice_region_variant nonsynonymous SNV ENSG00000177302 PASS FALSE TRUE TRUE TRUE TRUE 3.31 0.000786164 ENSG00000177302:ENST00000542570:exon4:c.A107T:p.K36I,ENSG00000177302:ENST00000321105:exon5:c.A392T:p.K131I,ENSG00000177302:ENST00000580095:exon5:c.A317T:p.K106I, 106 K/I 21,0 14,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0017 99 chr17:33443932:33443932:T:C:snp 0.675730396862748 0.102201257861636 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr17 33443932 33443932 T C snp nonsynonymous SNV RAD51D:NM_001142571:exon3:c.A269G:p.D90G, nonsynonymous SNV RAD51D missense_variant nonsynonymous SNV ENSG00000185379 PASS FALSE FALSE TRUE TRUE TRUE -3.38 0.00235849 ENSG00000185379:ENST00000590016:exon3:c.A269G:p.D90G, 90 D/G 23,0 14,0 0,1,144 0,2,489 0,1,139 0,2,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2935-03A-01W-0745-08 99 AOGC-02-0264,AOGC-08-0182 99,99 chr17:41197714:41197714:A:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41197714 41197714 A G snp nonsynonymous SNV BRCA1:NM_007300:exon24:c.T5636C:p.I1879T,BRCA1:NM_007297:exon22:c.T5432C:p.I1811T,BRCA1:NM_007298:exon22:c.T2261C:p.I754T,BRCA1:NM_007294:exon23:c.T5573C:p.I1858T, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS TRUE TRUE TRUE TRUE TRUE 0.223 0.000784929 ENSG00000012048:ENST00000351666:exon19:c.T2024C:p.I675T,ENSG00000012048:ENST00000491747:exon23:c.T2261C:p.I754T,ENSG00000012048:ENST00000591534:exon11:c.T1046C:p.I349T,ENSG00000012048:ENST00000309486:exon22:c.T4685C:p.I1562T,ENSG00000012048:ENST00000357654:exon23:c.T5573C:p.I1858T,ENSG00000012048:ENST00000591849:exon5:c.T272C:p.I91T,ENSG00000012048:ENST00000346315:exon19:c.T4856C:p.I1619T,ENSG00000012048:ENST00000352993:exon22:c.T2147C:p.I716T,ENSG00000012048:ENST00000354071:exon18:c.T4778C:p.I1593T,ENSG00000012048:ENST00000586385:exon8:c.T503C:p.I168T,ENSG00000012048:ENST00000493795:exon22:c.T5432C:p.I1811T,ENSG00000012048:ENST00000471181:exon24:c.T5636C:p.I1879T, 716 I/T 31,0 35,0 0,1,145 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2921-03A-01W-0755-09 99 chr17:41197757:41197757:G:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41197757 41197757 G T snp nonsynonymous SNV BRCA1:NM_007300:exon24:c.C5593A:p.L1865I,BRCA1:NM_007297:exon22:c.C5389A:p.L1797I,BRCA1:NM_007298:exon22:c.C2218A:p.L740I,BRCA1:NM_007294:exon23:c.C5530A:p.L1844I, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS TRUE TRUE TRUE TRUE TRUE 2.04 0.000784929 ENSG00000012048:ENST00000351666:exon19:c.C1981A:p.L661I,ENSG00000012048:ENST00000491747:exon23:c.C2218A:p.L740I,ENSG00000012048:ENST00000591534:exon11:c.C1003A:p.L335I,ENSG00000012048:ENST00000309486:exon22:c.C4642A:p.L1548I,ENSG00000012048:ENST00000357654:exon23:c.C5530A:p.L1844I,ENSG00000012048:ENST00000591849:exon5:c.C229A:p.L77I,ENSG00000012048:ENST00000346315:exon19:c.C4813A:p.L1605I,ENSG00000012048:ENST00000352993:exon22:c.C2104A:p.L702I,ENSG00000012048:ENST00000354071:exon18:c.C4735A:p.L1579I,ENSG00000012048:ENST00000586385:exon8:c.C460A:p.L154I,ENSG00000012048:ENST00000493795:exon22:c.C5389A:p.L1797I,ENSG00000012048:ENST00000471181:exon24:c.C5593A:p.L1865I, 702 L/I 31,0 35,0 0,1,145 0,0,491 0,1,144 0,0,462 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2900-03A-01W-0733-08 99 chr17:41197758:41197758:T:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41197758 41197758 T G snp synonymous SNV BRCA1:NM_007300:exon24:c.A5592C:p.A1864A,BRCA1:NM_007297:exon22:c.A5388C:p.A1796A,BRCA1:NM_007298:exon22:c.A2217C:p.A739A,BRCA1:NM_007294:exon23:c.A5529C:p.A1843A, synonymous SNV BRCA1 3_prime_UTR_variant synonymous SNV ENSG00000012048 PASS TRUE TRUE TRUE TRUE TRUE 4.34 0.000784929 ENSG00000012048:ENST00000351666:exon19:c.A1980C:p.A660A,ENSG00000012048:ENST00000491747:exon23:c.A2217C:p.A739A,ENSG00000012048:ENST00000591534:exon11:c.A1002C:p.A334A,ENSG00000012048:ENST00000309486:exon22:c.A4641C:p.A1547A,ENSG00000012048:ENST00000357654:exon23:c.A5529C:p.A1843A,ENSG00000012048:ENST00000591849:exon5:c.A228C:p.A76A,ENSG00000012048:ENST00000346315:exon19:c.A4812C:p.A1604A,ENSG00000012048:ENST00000352993:exon22:c.A2103C:p.A701A,ENSG00000012048:ENST00000354071:exon18:c.A4734C:p.A1578A,ENSG00000012048:ENST00000586385:exon8:c.A459C:p.A153A,ENSG00000012048:ENST00000493795:exon22:c.A5388C:p.A1796A,ENSG00000012048:ENST00000471181:exon24:c.A5592C:p.A1864A, - - 31,0 35,0 0,1,145 0,0,491 0,1,144 0,0,462 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2900-03A-01W-0733-08 99 chr17:41203065:41203065:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41203065 41203065 C G snp intronic BRCA1 intronic BRCA1 intron_variant intronic ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE 2.04 0.000786164 ENSG00000012048 - - 21,0 21,0 0,0,145 0,1,490 0,0,145 0,1,484 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0166 99 chr17:41223049:41223049:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41223049 41223049 T C snp nonsynonymous SNV BRCA1:NM_007300:exon16:c.A4945G:p.M1649V,BRCA1:NM_007297:exon14:c.A4741G:p.M1581V,BRCA1:NM_007298:exon14:c.A1570G:p.M524V,BRCA1:NM_007294:exon15:c.A4882G:p.M1628V,BRCA1:NM_007299:exon15:c.A1570G:p.M524V, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE -0.061 0.000788644 ENSG00000012048:ENST00000351666:exon11:c.A1333G:p.M445V,ENSG00000012048:ENST00000491747:exon15:c.A1570G:p.M524V,ENSG00000012048:ENST00000493919:exon14:c.A1432G:p.M478V,ENSG00000012048:ENST00000468300:exon15:c.A1570G:p.M524V,ENSG00000012048:ENST00000591534:exon3:c.A355G:p.M119V,ENSG00000012048:ENST00000309486:exon14:c.A3994G:p.M1332V,ENSG00000012048:ENST00000357654:exon15:c.A4882G:p.M1628V,ENSG00000012048:ENST00000352993:exon14:c.A1456G:p.M486V,ENSG00000012048:ENST00000478531:exon15:c.A1570G:p.M524V,ENSG00000012048:ENST00000484087:exon9:c.A1195G:p.M399V,ENSG00000012048:ENST00000493795:exon14:c.A4741G:p.M1581V,ENSG00000012048:ENST00000471181:exon16:c.A4945G:p.M1649V, 486 M/V 21,0 22,0 0,0,145 0,1,488 0,0,145 0,1,465 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0046 99 chr17:41226354:41226354:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41226354 41226354 C G snp nonsynonymous SNV BRCA1:NM_007300:exon15:c.G4732C:p.D1578H,BRCA1:NM_007297:exon13:c.G4528C:p.D1510H,BRCA1:NM_007298:exon13:c.G1357C:p.D453H,BRCA1:NM_007294:exon14:c.G4669C:p.D1557H,BRCA1:NM_007299:exon14:c.G1357C:p.D453H, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE 3.46 0.000784929 ENSG00000012048:ENST00000351666:exon10:c.G1120C:p.D374H,ENSG00000012048:ENST00000491747:exon14:c.G1357C:p.D453H,ENSG00000012048:ENST00000493919:exon13:c.G1219C:p.D407H,ENSG00000012048:ENST00000468300:exon14:c.G1357C:p.D453H,ENSG00000012048:ENST00000591534:exon2:c.G142C:p.D48H,ENSG00000012048:ENST00000309486:exon13:c.G3781C:p.D1261H,ENSG00000012048:ENST00000357654:exon14:c.G4669C:p.D1557H,ENSG00000012048:ENST00000352993:exon13:c.G1243C:p.D415H,ENSG00000012048:ENST00000478531:exon14:c.G1357C:p.D453H,ENSG00000012048:ENST00000484087:exon8:c.G982C:p.D328H,ENSG00000012048:ENST00000493795:exon13:c.G4528C:p.D1510H,ENSG00000012048:ENST00000471181:exon15:c.G4732C:p.D1578H, 415 D/H 20,0 24,0 0,0,146 0,1,490 0,0,145 0,1,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0340 99 chr17:41226488:41226488:C:A:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr17 41226488 41226488 C A snp nonsynonymous SNV BRCA1:NM_007300:exon15:c.G4598T:p.S1533I,BRCA1:NM_007297:exon13:c.G4394T:p.S1465I,BRCA1:NM_007298:exon13:c.G1223T:p.S408I,BRCA1:NM_007294:exon14:c.G4535T:p.S1512I,BRCA1:NM_007299:exon14:c.G1223T:p.S408I, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE FALSE TRUE TRUE TRUE 3.98 0.00156986 ENSG00000012048:ENST00000351666:exon10:c.G986T:p.S329I,ENSG00000012048:ENST00000491747:exon14:c.G1223T:p.S408I,ENSG00000012048:ENST00000493919:exon13:c.G1085T:p.S362I,ENSG00000012048:ENST00000468300:exon14:c.G1223T:p.S408I,ENSG00000012048:ENST00000591534:exon2:c.G8T:p.S3I,ENSG00000012048:ENST00000309486:exon13:c.G3647T:p.S1216I,ENSG00000012048:ENST00000357654:exon14:c.G4535T:p.S1512I,ENSG00000012048:ENST00000352993:exon13:c.G1109T:p.S370I,ENSG00000012048:ENST00000478531:exon14:c.G1223T:p.S408I,ENSG00000012048:ENST00000484087:exon8:c.G848T:p.S283I,ENSG00000012048:ENST00000493795:exon13:c.G4394T:p.S1465I,ENSG00000012048:ENST00000471181:exon15:c.G4598T:p.S1533I, 370 S/I 20,0 24,0 0,1,145 0,1,490 0,1,144 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2834-03B-01W-0728-08 99 AOGC-02-0465 99 chr17:41228587:41228587:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41228587 41228587 T G snp nonsynonymous SNV BRCA1:NM_007300:exon14:c.A4465C:p.N1489H,BRCA1:NM_007297:exon12:c.A4261C:p.N1421H,BRCA1:NM_007298:exon12:c.A1090C:p.N364H,BRCA1:NM_007294:exon13:c.A4402C:p.N1468H,BRCA1:NM_007299:exon13:c.A1090C:p.N364H, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE 3.86 0.000786164 ENSG00000012048:ENST00000487825:exon7:c.A718C:p.N240H,ENSG00000012048:ENST00000351666:exon9:c.A853C:p.N285H,ENSG00000012048:ENST00000491747:exon13:c.A1090C:p.N364H,ENSG00000012048:ENST00000493919:exon12:c.A952C:p.N318H,ENSG00000012048:ENST00000468300:exon13:c.A1090C:p.N364H,ENSG00000012048:ENST00000309486:exon12:c.A3514C:p.N1172H,ENSG00000012048:ENST00000357654:exon13:c.A4402C:p.N1468H,ENSG00000012048:ENST00000352993:exon12:c.A976C:p.N326H,ENSG00000012048:ENST00000478531:exon13:c.A1090C:p.N364H,ENSG00000012048:ENST00000484087:exon7:c.A715C:p.N239H,ENSG00000012048:ENST00000493795:exon12:c.A4261C:p.N1421H,ENSG00000012048:ENST00000471181:exon14:c.A4465C:p.N1489H, 326 N/H 32,0 20,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0237 99 chr17:41228679:41228679:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41228679 41228679 T C snp intronic BRCA1 intronic BRCA1 intron_variant intronic ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE 3.89 0.000787402 ENSG00000012048 - - 32,0 20,0 0,1,144 0,0,490 0,1,144 0,0,486 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2875-03A-01W-0732-08 99 chr17:41243416:41243416:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41243416 41243416 T C snp intronic BRCA1 intronic BRCA1 non_coding_exon_variant,nc_transcript_variant intronic ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE -10.3 0.000792393 ENSG00000012048 - - 28,0 20,0 0,1,144 0,0,486 0,1,144 0,0,398 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2901-03A-01W-0733-08 99 chr17:41243509:41243509:T:C:snp 0.811375565860404 -0.0321144674085843 0.134566185463994 0.00782472613458529 0.00782472613458529 1 1 0 chr17 41243509 41243509 T C snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.A4039G:p.R1347G,BRCA1:NM_007297:exon9:c.A3898G:p.R1300G,BRCA1:NM_007294:exon10:c.A4039G:p.R1347G, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE FALSE FALSE TRUE TRUE 2.98 0.00786164 ENSG00000012048:ENST00000309486:exon9:c.A3151G:p.R1051G,ENSG00000012048:ENST00000357654:exon10:c.A4039G:p.R1347G,ENSG00000012048:ENST00000346315:exon10:c.A4039G:p.R1347G,ENSG00000012048:ENST00000354071:exon10:c.A4039G:p.R1347G,ENSG00000012048:ENST00000493795:exon9:c.A3898G:p.R1300G,ENSG00000012048:ENST00000471181:exon10:c.A4039G:p.R1347G, 1347 R/G 28,0 20,0 0,2,143 0,8,483 0,2,143 0,7,477 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2833-03B-01W-0728-08,TCGA-AB-2933-03A-01W-0732-08 99,99 AOGC-02-0104,AOGC-02-0161,AOGC-02-0506,AOGC-03-0121,AOGC-03-0174,AOGC-08-0054,AOGC-08-0069,AOGC-08-0256 55,99,99,99,99,93,99,99 chr17:41243790:41243790:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41243790 41243790 G C snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.C3758G:p.S1253C,BRCA1:NM_007297:exon9:c.C3617G:p.S1206C,BRCA1:NM_007294:exon10:c.C3758G:p.S1253C, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE 4.35 0.000784929 ENSG00000012048:ENST00000309486:exon9:c.C2870G:p.S957C,ENSG00000012048:ENST00000357654:exon10:c.C3758G:p.S1253C,ENSG00000012048:ENST00000346315:exon10:c.C3758G:p.S1253C,ENSG00000012048:ENST00000354071:exon10:c.C3758G:p.S1253C,ENSG00000012048:ENST00000493795:exon9:c.C3617G:p.S1206C,ENSG00000012048:ENST00000471181:exon10:c.C3758G:p.S1253C, 1253 S/C 28,0 20,0 0,0,146 0,1,490 0,0,146 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0311 99 chr17:41244055:41244055:A:G:snp 0.068543172725465 0.384796238244514 0.211261777435397 0.00156494522691706 0.00156494522691706 1 1 0 chr17 41244055 41244055 A G snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.T3493C:p.F1165L,BRCA1:NM_007297:exon9:c.T3352C:p.F1118L,BRCA1:NM_007294:exon10:c.T3493C:p.F1165L, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS TRUE TRUE TRUE TRUE TRUE 5.31 0.0015674 ENSG00000012048:ENST00000309486:exon9:c.T2605C:p.F869L,ENSG00000012048:ENST00000357654:exon10:c.T3493C:p.F1165L,ENSG00000012048:ENST00000346315:exon10:c.T3493C:p.F1165L,ENSG00000012048:ENST00000354071:exon10:c.T3493C:p.F1165L,ENSG00000012048:ENST00000493795:exon9:c.T3352C:p.F1118L,ENSG00000012048:ENST00000471181:exon10:c.T3493C:p.F1165L, 1165 F/L 90,0 51,0 1,0,146 0,0,491 1,0,145 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2814-03B-01W-0728-08 9 chr17:41244252:41244252:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41244252 41244252 G A snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.C3296T:p.P1099L,BRCA1:NM_007297:exon9:c.C3155T:p.P1052L,BRCA1:NM_007294:exon10:c.C3296T:p.P1099L, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE FALSE TRUE TRUE TRUE 3.08 0.000784929 ENSG00000012048:ENST00000309486:exon9:c.C2408T:p.P803L,ENSG00000012048:ENST00000357654:exon10:c.C3296T:p.P1099L,ENSG00000012048:ENST00000346315:exon10:c.C3296T:p.P1099L,ENSG00000012048:ENST00000354071:exon10:c.C3296T:p.P1099L,ENSG00000012048:ENST00000493795:exon9:c.C3155T:p.P1052L,ENSG00000012048:ENST00000471181:exon10:c.C3296T:p.P1099L, 1099 P/L 90,0 51,0 0,0,146 0,1,490 0,0,146 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-05-0010 99 chr17:41244732:41244732:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41244732 41244732 A G snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.T2816C:p.V939A,BRCA1:NM_007297:exon9:c.T2675C:p.V892A,BRCA1:NM_007294:exon10:c.T2816C:p.V939A, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE FALSE TRUE TRUE TRUE 0.821 0.000786164 ENSG00000012048:ENST00000309486:exon9:c.T1928C:p.V643A,ENSG00000012048:ENST00000357654:exon10:c.T2816C:p.V939A,ENSG00000012048:ENST00000346315:exon10:c.T2816C:p.V939A,ENSG00000012048:ENST00000354071:exon10:c.T2816C:p.V939A,ENSG00000012048:ENST00000493795:exon9:c.T2675C:p.V892A,ENSG00000012048:ENST00000471181:exon10:c.T2816C:p.V939A, 939 V/A 120,0 84,0 0,0,146 0,1,489 0,0,145 0,1,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0170 99 chr17:41245027:41245027:G:A:snp 0.202168134675384 0.270078740157481 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr17 41245027 41245027 G A snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.C2521T:p.R841W,BRCA1:NM_007297:exon9:c.C2380T:p.R794W,BRCA1:NM_007294:exon10:c.C2521T:p.R841W, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE FALSE TRUE TRUE TRUE 2.84 0.00314465 ENSG00000012048:ENST00000309486:exon9:c.C1633T:p.R545W,ENSG00000012048:ENST00000357654:exon10:c.C2521T:p.R841W,ENSG00000012048:ENST00000346315:exon10:c.C2521T:p.R841W,ENSG00000012048:ENST00000354071:exon10:c.C2521T:p.R841W,ENSG00000012048:ENST00000493795:exon9:c.C2380T:p.R794W,ENSG00000012048:ENST00000471181:exon10:c.C2521T:p.R841W, 841 R/W 229,0 162,0 0,2,144 0,2,488 0,2,143 0,2,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2806-03B-01W-0728-08,TCGA-AB-2944-03A-01W-0755-09 99,99 AOGC-02-0092,AOGC-08-0196 99,99 chr17:41245136:41245136:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41245136 41245136 C G snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.G2412C:p.Q804H,BRCA1:NM_007297:exon9:c.G2271C:p.Q757H,BRCA1:NM_007294:exon10:c.G2412C:p.Q804H, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE FALSE TRUE TRUE TRUE -3.25 0.000788644 ENSG00000012048:ENST00000309486:exon9:c.G1524C:p.Q508H,ENSG00000012048:ENST00000357654:exon10:c.G2412C:p.Q804H,ENSG00000012048:ENST00000346315:exon10:c.G2412C:p.Q804H,ENSG00000012048:ENST00000354071:exon10:c.G2412C:p.Q804H,ENSG00000012048:ENST00000493795:exon9:c.G2271C:p.Q757H,ENSG00000012048:ENST00000471181:exon10:c.G2412C:p.Q804H, 804 Q/H 229,0 162,0 0,0,145 0,1,488 0,0,145 0,1,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0030 99 chr17:41245176:41245176:A:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41245176 41245176 A G snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.T2372C:p.L791P,BRCA1:NM_007297:exon9:c.T2231C:p.L744P,BRCA1:NM_007294:exon10:c.T2372C:p.L791P, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS TRUE TRUE TRUE TRUE TRUE -1.64 0.000788644 ENSG00000012048:ENST00000309486:exon9:c.T1484C:p.L495P,ENSG00000012048:ENST00000357654:exon10:c.T2372C:p.L791P,ENSG00000012048:ENST00000346315:exon10:c.T2372C:p.L791P,ENSG00000012048:ENST00000354071:exon10:c.T2372C:p.L791P,ENSG00000012048:ENST00000493795:exon9:c.T2231C:p.L744P,ENSG00000012048:ENST00000471181:exon10:c.T2372C:p.L791P, 791 L/P 229,0 162,0 0,1,144 0,0,489 0,1,144 0,0,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2860-03B-01W-0728-08 99 chr17:41245683:41245683:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41245683 41245683 G A snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.C1865T:p.A622V,BRCA1:NM_007297:exon9:c.C1724T:p.A575V,BRCA1:NM_007294:exon10:c.C1865T:p.A622V, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE 1.5 0.000784929 ENSG00000012048:ENST00000309486:exon9:c.C977T:p.A326V,ENSG00000012048:ENST00000357654:exon10:c.C1865T:p.A622V,ENSG00000012048:ENST00000346315:exon10:c.C1865T:p.A622V,ENSG00000012048:ENST00000470026:exon10:c.C1865T:p.A622V,ENSG00000012048:ENST00000477152:exon9:c.C1787T:p.A596V,ENSG00000012048:ENST00000354071:exon10:c.C1865T:p.A622V,ENSG00000012048:ENST00000493795:exon9:c.C1724T:p.A575V,ENSG00000012048:ENST00000471181:exon10:c.C1865T:p.A622V, 622 A/V 30,0 23,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0118 99 chr17:41245845:41245845:G:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr17 41245845 41245845 G A snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.C1703T:p.P568L,BRCA1:NM_007297:exon9:c.C1562T:p.P521L,BRCA1:NM_007294:exon10:c.C1703T:p.P568L, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE FALSE TRUE TRUE TRUE 4.09 0.00157233 ENSG00000012048:ENST00000309486:exon9:c.C815T:p.P272L,ENSG00000012048:ENST00000357654:exon10:c.C1703T:p.P568L,ENSG00000012048:ENST00000346315:exon10:c.C1703T:p.P568L,ENSG00000012048:ENST00000470026:exon10:c.C1703T:p.P568L,ENSG00000012048:ENST00000477152:exon9:c.C1625T:p.P542L,ENSG00000012048:ENST00000354071:exon10:c.C1703T:p.P568L,ENSG00000012048:ENST00000493795:exon9:c.C1562T:p.P521L,ENSG00000012048:ENST00000471181:exon10:c.C1703T:p.P568L, 568 P/L 30,0 23,0 0,0,145 0,2,489 0,0,145 0,2,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0249,AOGC-02-0250 99,99 chr17:41245900:41245900:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41245900 41245900 T G snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.A1648C:p.N550H,BRCA1:NM_007297:exon9:c.A1507C:p.N503H,BRCA1:NM_007294:exon10:c.A1648C:p.N550H, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE 1.32 0.000786164 ENSG00000012048:ENST00000309486:exon9:c.A760C:p.N254H,ENSG00000012048:ENST00000357654:exon10:c.A1648C:p.N550H,ENSG00000012048:ENST00000346315:exon10:c.A1648C:p.N550H,ENSG00000012048:ENST00000470026:exon10:c.A1648C:p.N550H,ENSG00000012048:ENST00000477152:exon9:c.A1570C:p.N524H,ENSG00000012048:ENST00000354071:exon10:c.A1648C:p.N550H,ENSG00000012048:ENST00000493795:exon9:c.A1507C:p.N503H,ENSG00000012048:ENST00000471181:exon10:c.A1648C:p.N550H, 550 N/H 30,0 23,0 0,0,146 0,1,489 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0099 99 chr17:41245967:41245967:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41245967 41245967 C G snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.G1581C:p.K527N,BRCA1:NM_007297:exon9:c.G1440C:p.K480N,BRCA1:NM_007294:exon10:c.G1581C:p.K527N, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE 0.357 0.000786164 ENSG00000012048:ENST00000309486:exon9:c.G693C:p.K231N,ENSG00000012048:ENST00000357654:exon10:c.G1581C:p.K527N,ENSG00000012048:ENST00000346315:exon10:c.G1581C:p.K527N,ENSG00000012048:ENST00000470026:exon10:c.G1581C:p.K527N,ENSG00000012048:ENST00000477152:exon9:c.G1503C:p.K501N,ENSG00000012048:ENST00000354071:exon10:c.G1581C:p.K527N,ENSG00000012048:ENST00000493795:exon9:c.G1440C:p.K480N,ENSG00000012048:ENST00000471181:exon10:c.G1581C:p.K527N, 527 K/N 30,0 22,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0009 99 chr17:41246062:41246062:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41246062 41246062 G A snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.C1486T:p.R496C,BRCA1:NM_007297:exon9:c.C1345T:p.R449C,BRCA1:NM_007294:exon10:c.C1486T:p.R496C, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE -0.308 0.000786164 ENSG00000012048:ENST00000309486:exon9:c.C598T:p.R200C,ENSG00000012048:ENST00000357654:exon10:c.C1486T:p.R496C,ENSG00000012048:ENST00000346315:exon10:c.C1486T:p.R496C,ENSG00000012048:ENST00000470026:exon10:c.C1486T:p.R496C,ENSG00000012048:ENST00000477152:exon9:c.C1408T:p.R470C,ENSG00000012048:ENST00000354071:exon10:c.C1486T:p.R496C,ENSG00000012048:ENST00000493795:exon9:c.C1345T:p.R449C,ENSG00000012048:ENST00000471181:exon10:c.C1486T:p.R496C, 496 R/C 30,0 24,0 0,1,144 0,0,491 0,1,144 0,0,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2880-03A-01W-0732-08 99 chr17:41246092:41246092:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41246092 41246092 A G snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.T1456C:p.F486L,BRCA1:NM_007297:exon9:c.T1315C:p.F439L,BRCA1:NM_007294:exon10:c.T1456C:p.F486L, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE -3.69 0.000786164 ENSG00000012048:ENST00000309486:exon9:c.T568C:p.F190L,ENSG00000012048:ENST00000357654:exon10:c.T1456C:p.F486L,ENSG00000012048:ENST00000346315:exon10:c.T1456C:p.F486L,ENSG00000012048:ENST00000470026:exon10:c.T1456C:p.F486L,ENSG00000012048:ENST00000477152:exon9:c.T1378C:p.F460L,ENSG00000012048:ENST00000354071:exon10:c.T1456C:p.F486L,ENSG00000012048:ENST00000493795:exon9:c.T1315C:p.F439L,ENSG00000012048:ENST00000471181:exon10:c.T1456C:p.F486L, 486 F/L 30,0 24,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0099 99 chr17:41246547:41246547:G:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr17 41246547 41246547 G A snp nonsynonymous SNV BRCA1:NM_007300:exon10:c.C1001T:p.P334L,BRCA1:NM_007297:exon9:c.C860T:p.P287L,BRCA1:NM_007294:exon10:c.C1001T:p.P334L, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE FALSE TRUE TRUE TRUE 1.86 0.00157233 ENSG00000012048:ENST00000309486:exon9:c.C113T:p.P38L,ENSG00000012048:ENST00000357654:exon10:c.C1001T:p.P334L,ENSG00000012048:ENST00000494123:exon10:c.C1001T:p.P334L,ENSG00000012048:ENST00000346315:exon10:c.C1001T:p.P334L,ENSG00000012048:ENST00000497488:exon2:c.C113T:p.P38L,ENSG00000012048:ENST00000470026:exon10:c.C1001T:p.P334L,ENSG00000012048:ENST00000477152:exon9:c.C923T:p.P308L,ENSG00000012048:ENST00000354071:exon10:c.C1001T:p.P334L,ENSG00000012048:ENST00000493795:exon9:c.C860T:p.P287L,ENSG00000012048:ENST00000471181:exon10:c.C1001T:p.P334L, 334 P/L 30,0 27,0 0,0,145 0,2,489 0,0,145 0,2,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0087,AOGC-02-0105 99,99 chr17:41251803:41251803:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 41251803 41251803 T C snp nonsynonymous SNV BRCA1:NM_007300:exon7:c.A536G:p.Y179C,BRCA1:NM_007297:exon6:c.A395G:p.Y132C,BRCA1:NM_007298:exon6:c.A536G:p.Y179C,BRCA1:NM_007294:exon7:c.A536G:p.Y179C,BRCA1:NM_007299:exon7:c.A536G:p.Y179C, nonsynonymous SNV BRCA1 missense_variant nonsynonymous SNV ENSG00000012048 PASS FALSE TRUE TRUE TRUE TRUE 5.16 0.000784929 ENSG00000012048:ENST00000487825:exon3:c.A284G:p.Y95C,ENSG00000012048:ENST00000351666:exon6:c.A536G:p.Y179C,ENSG00000012048:ENST00000491747:exon7:c.A536G:p.Y179C,ENSG00000012048:ENST00000493919:exon6:c.A395G:p.Y132C,ENSG00000012048:ENST00000468300:exon7:c.A536G:p.Y179C,ENSG00000012048:ENST00000357654:exon7:c.A536G:p.Y179C,ENSG00000012048:ENST00000494123:exon7:c.A536G:p.Y179C,ENSG00000012048:ENST00000346315:exon7:c.A536G:p.Y179C,ENSG00000012048:ENST00000352993:exon7:c.A536G:p.Y179C,ENSG00000012048:ENST00000478531:exon7:c.A533G:p.Y178C,ENSG00000012048:ENST00000476777:exon7:c.A533G:p.Y178C,ENSG00000012048:ENST00000470026:exon7:c.A536G:p.Y179C,ENSG00000012048:ENST00000477152:exon6:c.A458G:p.Y153C,ENSG00000012048:ENST00000354071:exon7:c.A536G:p.Y179C,ENSG00000012048:ENST00000484087:exon3:c.A281G:p.Y94C,ENSG00000012048:ENST00000493795:exon6:c.A395G:p.Y132C,ENSG00000012048:ENST00000471181:exon7:c.A536G:p.Y179C, 179 Y/C 26,0 20,0 0,0,146 0,1,490 0,0,145 0,1,484 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0099 99 chr17:48455933:48455933:C:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr17 48455933 48455933 C A snp intronic EME1 intronic EME1 intron_variant intronic ENSG00000154920 PASS FALSE FALSE TRUE TRUE TRUE 3.59 0.00157233 ENSG00000108829,ENSG00000154920 - - 21,0 31,0 0,0,145 0,2,489 0,0,145 0,2,489 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0284,AOGC-14-0093 99,99 chr17:48456140:48456140:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 48456140 48456140 C G snp nonsynonymous SNV EME1:NM_152463:exon5:c.C996G:p.S332R,EME1:NM_001166131:exon5:c.C996G:p.S332R, nonsynonymous SNV EME1 missense_variant nonsynonymous SNV ENSG00000154920 PASS FALSE TRUE TRUE TRUE TRUE -3.79 0.000784929 ENSG00000154920:ENST00000393271:exon5:c.C996G:p.S332R,ENSG00000154920:ENST00000511648:exon4:c.C996G:p.S332R,ENSG00000154920:ENST00000338165:exon5:c.C996G:p.S332R, 332 S/R 21,0 49,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0069 99 chr17:48456471:48456471:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 48456471 48456471 T G snp synonymous SNV EME1:NM_152463:exon6:c.T1116G:p.A372A,EME1:NM_001166131:exon6:c.T1155G:p.A385A, synonymous SNV EME1 non_coding_exon_variant,nc_transcript_variant synonymous SNV ENSG00000154920 PASS FALSE TRUE TRUE TRUE TRUE 3.06 0.000786164 ENSG00000154920:ENST00000393271:exon6:c.T1155G:p.A385A,ENSG00000154920:ENST00000511648:exon5:c.T1155G:p.A385A,ENSG00000154920:ENST00000338165:exon6:c.T1116G:p.A372A, - - 23,0 21,0 0,0,145 0,1,490 0,0,145 0,1,490 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0077 99 chr17:48456520:48456520:A:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 48456520 48456520 A C snp nonsynonymous SNV EME1:NM_152463:exon6:c.A1165C:p.K389Q,EME1:NM_001166131:exon6:c.A1204C:p.K402Q, nonsynonymous SNV EME1 missense_variant nonsynonymous SNV ENSG00000154920 PASS FALSE TRUE TRUE TRUE TRUE 0.921 0.000786164 ENSG00000154920:ENST00000393271:exon6:c.A1204C:p.K402Q,ENSG00000154920:ENST00000511648:exon5:c.A1204C:p.K402Q,ENSG00000154920:ENST00000338165:exon6:c.A1165C:p.K389Q, 402 K/Q 23,0 21,0 0,0,145 0,1,490 0,0,144 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0059 99 chr17:48456559:48456559:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 48456559 48456559 A G snp nonsynonymous SNV EME1:NM_152463:exon6:c.A1204G:p.M402V,EME1:NM_001166131:exon6:c.A1243G:p.M415V, nonsynonymous SNV EME1 missense_variant nonsynonymous SNV ENSG00000154920 PASS FALSE TRUE TRUE TRUE TRUE -7.4 0.000786164 ENSG00000154920:ENST00000393271:exon6:c.A1243G:p.M415V,ENSG00000154920:ENST00000511648:exon5:c.A1243G:p.M415V,ENSG00000154920:ENST00000338165:exon6:c.A1204G:p.M402V, 415 M/V 23,0 21,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0041 99 chr17:48456849:48456849:G:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr17 48456849 48456849 G A snp nonsynonymous SNV EME1:NM_152463:exon7:c.G1267A:p.A423T,EME1:NM_001166131:exon7:c.G1306A:p.A436T, nonsynonymous SNV EME1 missense_variant nonsynonymous SNV ENSG00000154920 PASS FALSE FALSE TRUE TRUE TRUE 4.63 0.00157233 ENSG00000154920:ENST00000393271:exon7:c.G1306A:p.A436T,ENSG00000154920:ENST00000511648:exon6:c.G1306A:p.A436T,ENSG00000154920:ENST00000338165:exon7:c.G1267A:p.A423T, 436 A/T 23,0 21,0 0,0,145 0,2,489 0,0,144 0,2,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0269,AOGC-03-0167 99,99 chr17:48457819:48457819:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 48457819 48457819 G A snp nonsynonymous SNV EME1:NM_152463:exon8:c.G1493A:p.S498N,EME1:NM_001166131:exon8:c.G1532A:p.S511N, nonsynonymous SNV EME1 missense_variant nonsynonymous SNV ENSG00000154920 PASS FALSE TRUE TRUE TRUE TRUE 3.93 0.000786164 ENSG00000154920:ENST00000393271:exon8:c.G1532A:p.S511N,ENSG00000154920:ENST00000511648:exon7:c.G1532A:p.S511N,ENSG00000154920:ENST00000338165:exon8:c.G1493A:p.S498N, 511 S/N 21,0 23,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0207 99 chr17:48457844:48457844:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 48457844 48457844 C T snp synonymous SNV EME1:NM_152463:exon8:c.C1518T:p.S506S,EME1:NM_001166131:exon8:c.C1557T:p.S519S, synonymous SNV EME1 non_coding_exon_variant,nc_transcript_variant synonymous SNV ENSG00000154920 PASS FALSE FALSE TRUE TRUE TRUE 2.69 0.000786164 ENSG00000154920:ENST00000393271:exon8:c.C1557T:p.S519S,ENSG00000154920:ENST00000511648:exon7:c.C1557T:p.S519S,ENSG00000154920:ENST00000338165:exon8:c.C1518T:p.S506S, - - 21,0 23,0 0,1,144 0,0,491 0,1,144 0,0,486 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2872-03A-01W-0732-08 99 chr17:56770101:56770101:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 56770101 56770101 C T snp stopgain SNV RAD51C:NM_058216:exon1:c.C97T:p.Q33X,RAD51C:NM_002876:exon1:c.C97T:p.Q33X, stopgain SNV RAD51C stop_gained,NMD_transcript_variant stopgain SNV ENSG00000108384 PASS TRUE TRUE TRUE TRUE TRUE 4.75 0.000811688 ENSG00000108384:ENST00000421782:exon1:c.C97T:p.Q33X,ENSG00000108384:ENST00000486827:exon1:c.C97T:p.Q33X,ENSG00000108384:ENST00000482007:exon1:c.C97T:p.Q33X,ENSG00000108384:ENST00000487525:exon1:c.C97T:p.Q33X,ENSG00000108384:ENST00000583539:exon1:c.C97T:p.Q33X,ENSG00000108384:ENST00000475762:exon1:c.C97T:p.Q33X,ENSG00000108384:ENST00000337432:exon1:c.C97T:p.Q33X, 27 Q/* 21,0 39,0 0,1,144 0,0,471 0,1,144 0,0,413 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2823-03B-01W-0728-08 99 chr17:56772284:56772284:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 56772284 56772284 A G snp intronic RAD51C intronic RAD51C splice_region_variant,intron_variant intronic ENSG00000108384 PASS FALSE FALSE TRUE TRUE TRUE 0.181 0.000787402 ENSG00000108384 - - 28,0 22,0 0,0,145 0,1,489 0,0,145 0,1,477 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0258 99 chr17:56772522:56772522:G:A:snp 0.866515946988662 -0.0318611987381696 0.189553423814011 0.00391236306729264 0.00391236306729264 1 1 0 chr17 56772522 56772522 G A snp nonsynonymous SNV RAD51C:NM_058216:exon2:c.G376A:p.A126T,RAD51C:NM_002876:exon2:c.G376A:p.A126T, nonsynonymous SNV RAD51C missense_variant nonsynonymous SNV ENSG00000108384 PASS FALSE FALSE FALSE TRUE TRUE 3.35 0.0039557 ENSG00000108384:ENST00000425173:exon1:c.G172A:p.A58T,ENSG00000108384:ENST00000421782:exon2:c.G376A:p.A126T,ENSG00000108384:ENST00000482007:exon2:c.G376A:p.A126T,ENSG00000108384:ENST00000487525:exon2:c.G376A:p.A126T,ENSG00000108384:ENST00000583539:exon2:c.G376A:p.A126T,ENSG00000108384:ENST00000337432:exon2:c.G376A:p.A126T,ENSG00000108384:ENST00000461271:exon2:c.G25A:p.A9T, 58 A/T 28,0 22,0 0,1,144 0,4,483 0,1,144 0,4,461 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2896-03A-01W-0733-08 99 AOGC-02-0205,AOGC-02-0441,AOGC-08-0205,AOGC-08-0239 99,99,99,99 chr17:56787235:56787235:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 56787235 56787235 G A snp nonsynonymous SNV RAD51C:NM_058216:exon5:c.G721A:p.V241M, nonsynonymous SNV RAD51C missense_variant nonsynonymous SNV ENSG00000108384 PASS FALSE TRUE TRUE TRUE TRUE 5.03 0.000786164 ENSG00000108384:ENST00000584804:exon1:c.G16A:p.V6M,ENSG00000108384:ENST00000425173:exon5:c.G637A:p.V213M,ENSG00000108384:ENST00000583539:exon5:c.G721A:p.V241M,ENSG00000108384:ENST00000337432:exon5:c.G721A:p.V241M,ENSG00000108384:ENST00000461271:exon5:c.G370A:p.V124M, 241 V/M 23,0 23,0 0,1,144 0,0,491 0,1,144 0,0,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2881-03A-01W-0732-08 99 chr17:56787253:56787253:C:T:snp 0.27105525402704 -0.233070866141732 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr17 56787253 56787253 C T snp nonsynonymous SNV RAD51C:NM_058216:exon5:c.C739T:p.P247S, nonsynonymous SNV RAD51C missense_variant nonsynonymous SNV ENSG00000108384 PASS TRUE TRUE TRUE TRUE TRUE 6 0.00313972 ENSG00000108384:ENST00000584804:exon1:c.C34T:p.P12S,ENSG00000108384:ENST00000583539:exon5:c.C739T:p.P247S,ENSG00000108384:ENST00000337432:exon5:c.C739T:p.P247S,ENSG00000108384:ENST00000461271:exon5:c.C388T:p.P130S, 247 P/S 25,0 23,0 0,0,146 0,4,487 0,0,145 0,4,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0190,AOGC-02-0397,AOGC-02-0530,AOGC-08-0033 62,27,76,22 chr17:56787287:56787287:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 56787287 56787287 G A snp nonsynonymous SNV RAD51C:NM_058216:exon5:c.G773A:p.R258H, nonsynonymous SNV RAD51C missense_variant nonsynonymous SNV ENSG00000108384 PASS FALSE TRUE TRUE TRUE TRUE 6 0.000784929 ENSG00000108384:ENST00000584804:exon1:c.G68A:p.R23H,ENSG00000108384:ENST00000583539:exon5:c.G773A:p.R258H,ENSG00000108384:ENST00000337432:exon5:c.G773A:p.R258H, 258 R/H 25,0 23,0 0,0,146 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0284 99 chr17:56787304:56787304:G:A:snp 0.553207497378776 0.102685624012639 0.173174436921412 0.00469483568075117 0.00469483568075117 1 1 0 chr17 56787304 56787304 G A snp nonsynonymous SNV RAD51C:NM_058216:exon5:c.G790A:p.G264S, nonsynonymous SNV RAD51C missense_variant nonsynonymous SNV ENSG00000108384 PASS FALSE FALSE TRUE TRUE TRUE 6 0.00470958 ENSG00000108384:ENST00000584804:exon1:c.G85A:p.G29S,ENSG00000108384:ENST00000583539:exon5:c.G790A:p.G264S,ENSG00000108384:ENST00000337432:exon5:c.G790A:p.G264S, 264 G/S 25,0 23,0 0,2,144 0,4,487 0,2,143 0,4,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2812-03B-01W-0728-08,TCGA-AB-2933-03A-01W-0732-08 99,99 AOGC-02-0141,AOGC-02-0369,AOGC-03-0152,AOGC-08-0319 99,99,97,99 chr17:59853755:59853755:C:T:snp 0.930368235661057 0.0185039370078748 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr17 59853755 59853755 C T snp intronic BRIP1 intronic BRIP1 splice_region_variant,intron_variant intronic ENSG00000136492 PASS FALSE FALSE TRUE TRUE TRUE 1.76 0.00314961 ENSG00000136492 - - 22,0 25,0 0,1,144 0,3,487 0,1,144 0,2,449 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2842-03A-01W-0726-08 99 AOGC-02-0467,AOGC-03-0001,AOGC-08-0126 99,99,68 chr17:59857721:59857721:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 59857721 59857721 C T snp synonymous SNV BRIP1:NM_032043:exon13:c.G1836A:p.L612L, synonymous SNV BRIP1 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000136492 PASS FALSE TRUE TRUE TRUE TRUE 3.61 0.000787402 ENSG00000136492:ENST00000259008:exon13:c.G1836A:p.L612L,ENSG00000136492:ENST00000577598:exon12:c.G1836A:p.L612L, - - 32,0 26,0 0,0,145 0,1,489 0,0,145 0,1,478 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0535 99 chr17:59858236:59858236:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 59858236 59858236 G C snp nonsynonymous SNV BRIP1:NM_032043:exon12:c.C1759G:p.H587D, nonsynonymous SNV BRIP1 missense_variant nonsynonymous SNV ENSG00000136492 PASS FALSE TRUE TRUE TRUE TRUE 3.29 0.000787402 ENSG00000136492:ENST00000259008:exon12:c.C1759G:p.H587D,ENSG00000136492:ENST00000577598:exon11:c.C1759G:p.H587D, 587 H/D 26,0 23,0 0,0,146 0,1,488 0,0,145 0,1,445 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0305 99 chr17:59876546:59876546:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 59876546 59876546 G A snp nonsynonymous SNV BRIP1:NM_032043:exon9:c.C1255T:p.R419W, nonsynonymous SNV BRIP1 missense_variant nonsynonymous SNV ENSG00000136492 PASS FALSE FALSE TRUE TRUE TRUE 3.54 0.000784929 ENSG00000136492:ENST00000259008:exon9:c.C1255T:p.R419W,ENSG00000136492:ENST00000577598:exon8:c.C1255T:p.R419W, 419 R/W 21,0 21,0 0,0,146 0,1,490 0,0,146 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0136 99 chr17:59886085:59886085:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 59886085 59886085 T C snp nonsynonymous SNV BRIP1:NM_032043:exon7:c.A661G:p.T221A, nonsynonymous SNV BRIP1 missense_variant nonsynonymous SNV ENSG00000136492 PASS FALSE TRUE TRUE TRUE TRUE 1.68 0.000784929 ENSG00000136492:ENST00000259008:exon7:c.A661G:p.T221A,ENSG00000136492:ENST00000577598:exon6:c.A661G:p.T221A, 221 T/A 23,0 22,0 0,0,146 0,1,490 0,0,145 0,1,461 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-05-0010 99 chr17:59886116:59886116:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 59886116 59886116 G A snp synonymous SNV BRIP1:NM_032043:exon7:c.C630T:p.P210P, synonymous SNV BRIP1 splice_region_variant,synonymous_variant synonymous SNV ENSG00000136492 PASS TRUE TRUE TRUE TRUE TRUE -5.55 0.000786164 ENSG00000136492:ENST00000259008:exon7:c.C630T:p.P210P,ENSG00000136492:ENST00000577598:exon6:c.C630T:p.P210P, 210 P 23,0 22,0 0,1,145 0,0,490 0,1,144 0,0,442 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2870-03A-01W-0732-08 99 chr17:59924505:59924505:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 59924505 59924505 A G snp nonsynonymous SNV BRIP1:NM_032043:exon6:c.T584C:p.L195P, nonsynonymous SNV BRIP1 missense_variant nonsynonymous SNV ENSG00000136492 PASS FALSE FALSE TRUE TRUE TRUE -0.0114 0.000786164 ENSG00000136492:ENST00000259008:exon6:c.T584C:p.L195P,ENSG00000136492:ENST00000577598:exon5:c.T584C:p.L195P, 195 L/P 22,0 21,0 0,0,146 0,1,489 0,0,145 0,1,477 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0158 99 chr17:59924512:59924512:C:T:snp 0.946425971912601 -0.00952380952380877 0.141732593760593 0.00704225352112676 0.00704225352112676 1 1 0 chr17 59924512 59924512 C T snp nonsynonymous SNV BRIP1:NM_032043:exon6:c.G577A:p.V193I, nonsynonymous SNV BRIP1 missense_variant nonsynonymous SNV ENSG00000136492 PASS FALSE FALSE FALSE TRUE TRUE -8.22 0.00708661 ENSG00000136492:ENST00000259008:exon6:c.G577A:p.V193I,ENSG00000136492:ENST00000577598:exon5:c.G577A:p.V193I, 193 V/I 22,0 21,0 0,2,143 0,7,483 0,2,143 0,7,471 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2816-03B-01W-0728-08,TCGA-AB-2847-03B-01W-0728-08 99,99 AOGC-02-0120,AOGC-02-0304,AOGC-02-0370,AOGC-02-0522,AOGC-03-0142,AOGC-08-0048,AOGC-08-0170 99,99,67,99,99,39,99 chr17:59924572:59924572:G:A:snp 0.946425971912601 -0.00952380952380877 0.141732593760593 0.00704225352112676 0.00704225352112676 1 1 0 chr17 59924572 59924572 G A snp nonsynonymous SNV BRIP1:NM_032043:exon6:c.C517T:p.R173C, nonsynonymous SNV BRIP1 missense_variant nonsynonymous SNV ENSG00000136492 PASS FALSE FALSE FALSE TRUE TRUE 5.26 0.00709779 ENSG00000136492:ENST00000259008:exon6:c.C517T:p.R173C,ENSG00000136492:ENST00000577598:exon5:c.C517T:p.R173C, 173 R/C 22,0 21,0 0,2,143 0,7,482 0,2,143 0,7,464 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2808-03D-01W-0755-09,TCGA-AB-2888-03A-01W-0732-08 99,99 AOGC-02-0078,AOGC-02-0522,AOGC-03-0084,AOGC-05-0008,AOGC-05-0021,AOGC-08-0170,AOGC-08-0210 99,99,99,99,99,99,99 chr17:59938933:59938933:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 59938933 59938933 A G snp splicing BRIP1 splicing BRIP1 splice_region_variant,intron_variant splicing ENSG00000136492 PASS FALSE FALSE TRUE TRUE TRUE 3.31 0.000791139 ENSG00000136492 - - 20,0 21,0 0,0,145 0,1,486 0,0,145 0,1,461 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0254 99 chr17:79517718:79517718:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 79517718 79517718 G A snp nonsynonymous SNV C17orf70:NM_025161:exon3:c.C802T:p.P268S, nonsynonymous SNV C17orf70 missense_variant nonsynonymous SNV ENSG00000185504 PASS FALSE TRUE TRUE TRUE TRUE 3.38 0.000787402 ENSG00000185504:ENST00000544302:exon3:c.C349T:p.P117S,ENSG00000185504:ENST00000537152:exon3:c.C349T:p.P117S,ENSG00000185504:ENST00000327787:exon3:c.C802T:p.P268S,ENSG00000185504:ENST00000541246:exon2:c.C349T:p.P117S, 117 P/S 9,0 7,0 0,0,144 0,1,490 0,0,140 0,1,469 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0281 99 chr17:79517729:79517729:G:A:snp 0.0137620143357551 0.521653543307087 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr17 79517729 79517729 G A snp nonsynonymous SNV C17orf70:NM_025161:exon3:c.C791T:p.A264V, nonsynonymous SNV C17orf70 missense_variant nonsynonymous SNV ENSG00000185504 PASS FALSE FALSE TRUE TRUE TRUE 1.27 0.00315457 ENSG00000185504:ENST00000544302:exon3:c.C338T:p.A113V,ENSG00000185504:ENST00000537152:exon3:c.C338T:p.A113V,ENSG00000185504:ENST00000327787:exon3:c.C791T:p.A264V,ENSG00000185504:ENST00000541246:exon2:c.C338T:p.A113V, 113 A/V 9,0 7,0 0,3,140 0,1,490 0,3,136 0,1,469 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2866-03B-01W-0728-08,TCGA-AB-2887-03A-01W-0732-08,TCGA-AB-2949-03A-01W-0733-08 99,99,99 AOGC-03-0129 99 chr17:41244049:41244049:-:TGAACTCGGGCTGA:indel 0.068543172725465 0.384796238244514 0.211261777435397 0.00156494522691706 0.00156494522691706 1 1 0 chr17 41244049 41244049 - TGAACTCGGGCTGA indel frameshift insertion BRCA1:NM_007300:exon10:c.3499_3500insTCAGCCCGAGTTCA:p.E1167fs,BRCA1:NM_007297:exon9:c.3358_3359insTCAGCCCGAGTTCA:p.E1120fs,BRCA1:NM_007294:exon10:c.3499_3500insTCAGCCCGAGTTCA:p.E1167fs, frameshift insertion BRCA1 frameshift_variant,feature_elongation frameshift insertion ENSG00000012048 PASS TRUE TRUE TRUE TRUE TRUE 4.23 0.0015674 ENSG00000012048:ENST00000309486:exon9:c.2611_2612insTCAGCCCGAGTTCA:p.E871fs,ENSG00000012048:ENST00000357654:exon10:c.3499_3500insTCAGCCCGAGTTCA:p.E1167fs,ENSG00000012048:ENST00000346315:exon10:c.3499_3500insTCAGCCCGAGTTCA:p.E1167fs,ENSG00000012048:ENST00000354071:exon10:c.3499_3500insTCAGCCCGAGTTCA:p.E1167fs,ENSG00000012048:ENST00000493795:exon9:c.3358_3359insTCAGCCCGAGTTCA:p.E1120fs,ENSG00000012048:ENST00000471181:exon10:c.3499_3500insTCAGCCCGAGTTCA:p.E1167fs, 1166-1167 - 90,0 51,0 1,0,146 0,0,491 1,0,145 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2814-03B-01W-0728-08 9 chr17:41244052:41244052:-:CCG:indel 0.068543172725465 0.384796238244514 0.211261777435397 0.00156494522691706 0.00156494522691706 1 1 0 chr17 41244052 41244052 - CCG indel nonframeshift insertion BRCA1:NM_007300:exon10:c.3496_3497insCGG:p.A1166delinsRA,BRCA1:NM_007297:exon9:c.3355_3356insCGG:p.A1119delinsRA,BRCA1:NM_007294:exon10:c.3496_3497insCGG:p.A1166delinsRA, nonframeshift insertion BRCA1 inframe_insertion nonframeshift insertion ENSG00000012048 PASS TRUE TRUE TRUE TRUE TRUE 1.76 0.0015674 ENSG00000012048:ENST00000309486:exon9:c.2608_2609insCGG:p.A870delinsRA,ENSG00000012048:ENST00000357654:exon10:c.3496_3497insCGG:p.A1166delinsRA,ENSG00000012048:ENST00000346315:exon10:c.3496_3497insCGG:p.A1166delinsRA,ENSG00000012048:ENST00000354071:exon10:c.3496_3497insCGG:p.A1166delinsRA,ENSG00000012048:ENST00000493795:exon9:c.3355_3356insCGG:p.A1119delinsRA,ENSG00000012048:ENST00000471181:exon10:c.3496_3497insCGG:p.A1166delinsRA, 1165-1166 -/R 90,0 51,0 1,0,146 0,0,491 1,0,145 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2814-03B-01W-0728-08 9 chr17:41244053:41244053:-:GCTGTTGCGTGCTGT:indel 0.068543172725465 0.384796238244514 0.211261777435397 0.00156494522691706 0.00156494522691706 1 1 0 chr17 41244053 41244053 - GCTGTTGCGTGCTGT indel nonframeshift insertion BRCA1:NM_007300:exon10:c.3495_3496insACAGCACGCAACAGC:p.F1165delinsLQHATA,BRCA1:NM_007297:exon9:c.3354_3355insACAGCACGCAACAGC:p.F1118delinsLQHATA,BRCA1:NM_007294:exon10:c.3495_3496insACAGCACGCAACAGC:p.F1165delinsLQHATA, nonframeshift insertion BRCA1 missense_variant,feature_elongation nonframeshift insertion ENSG00000012048 PASS TRUE TRUE TRUE TRUE TRUE 5.31 0.0015674 ENSG00000012048:ENST00000309486:exon9:c.2607_2608insACAGCACGCAACAGC:p.F869delinsLQHATA,ENSG00000012048:ENST00000357654:exon10:c.3495_3496insACAGCACGCAACAGC:p.F1165delinsLQHATA,ENSG00000012048:ENST00000346315:exon10:c.3495_3496insACAGCACGCAACAGC:p.F1165delinsLQHATA,ENSG00000012048:ENST00000354071:exon10:c.3495_3496insACAGCACGCAACAGC:p.F1165delinsLQHATA,ENSG00000012048:ENST00000493795:exon9:c.3354_3355insACAGCACGCAACAGC:p.F1118delinsLQHATA,ENSG00000012048:ENST00000471181:exon10:c.3495_3496insACAGCACGCAACAGC:p.F1165delinsLQHATA, 1165 F/LQHATA 90,0 51,0 1,0,146 0,0,491 1,0,145 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2814-03B-01W-0728-08 9 chr17:56772369:56772369:-:A:indel 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr17 56772369 56772369 - A indel stopgain SNV RAD51C:NM_058216:exon2:c.223_224insA:p.Y75_A76delinsX,RAD51C:NM_002876:exon2:c.223_224insA:p.Y75_A76delinsX, stopgain SNV RAD51C frameshift_variant,feature_elongation stopgain SNV ENSG00000108384 PASS TRUE TRUE TRUE TRUE TRUE 2.47 0.000786164 ENSG00000108384:ENST00000425173:exon1:c.19_20insA:p.Y7_A8delinsX,ENSG00000108384:ENST00000421782:exon2:c.223_224insA:p.Y75_A76delinsX,ENSG00000108384:ENST00000482007:exon2:c.223_224insA:p.Y75_A76delinsX,ENSG00000108384:ENST00000487525:exon2:c.223_224insA:p.Y75_A76delinsX,ENSG00000108384:ENST00000583539:exon2:c.223_224insA:p.Y75_A76delinsX,ENSG00000108384:ENST00000337432:exon2:c.223_224insA:p.Y75_A76delinsX, 7 - 28,0 22,0 0,1,144 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2833-03B-01W-0728-08 99 chr17:56772612:56772612:-:GTACTATCG:indel 0.0651349089757795 0.20284621920136 0.109983627479497 0.0101721439749609 0.0101721439749609 1 1 0 chr17 56772612 56772612 - GTACTATCG indel UTR3 RAD51C UTR3 RAD51C 3_prime_UTR_variant,feature_elongation UTR3 ENSG00000108384 PASS TRUE TRUE TRUE TRUE TRUE 3.31 0.0106036 ENSG00000108384 - - 28,0 9,0 1,4,140 0,7,461 1,4,140 0,5,430 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2812-03B-01W-0728-08,TCGA-AB-2824-03B-01W-0728-08,TCGA-AB-2854-03B-01W-0728-08,TCGA-AB-2889-03A-01W-0732-08,TCGA-AB-2921-03A-01W-0755-09 99,99,99,99,99 AOGC-02-0064,AOGC-02-0155,AOGC-02-0161,AOGC-02-0281,AOGC-05-0019,AOGC-08-0218,AOGC-08-0229 48,69,99,99,99,99,99 chr17:59821967:59821967:-:A:indel 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr17 59821967 59821967 - A indel intronic BRIP1 intronic BRIP1 intron_variant,feature_elongation intronic ENSG00000136492 PASS TRUE TRUE TRUE TRUE TRUE 2.87 0.00157729 ENSG00000136492 - - 32,0 25,0 0,0,146 0,2,486 0,0,146 0,2,449 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0522,AOGC-08-0170 99,99 chr19:33464448:33464448:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr19 33464448 33464448 A G snp nonsynonymous SNV C19orf40:NM_152266:exon3:c.A223G:p.I75V, nonsynonymous SNV C19orf40 missense_variant nonsynonymous SNV ENSG00000131944 PASS FALSE TRUE TRUE TRUE TRUE 4.68 0.000787402 ENSG00000131944:ENST00000590281:exon3:c.A223G:p.R75G,ENSG00000131944:ENST00000588258:exon3:c.A223G:p.R75G, 75 R/G 34,0 25,0 0,0,145 0,1,489 0,0,145 0,1,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0130 99 chr19:45916814:45916814:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr19 45916814 45916814 G A snp nonsynonymous SNV ERCC1:NM_202001:exon8:c.C964T:p.R322C, nonsynonymous SNV ERCC1 missense_variant nonsynonymous SNV ENSG00000012061 PASS FALSE FALSE TRUE TRUE TRUE -1.78 0.000786164 ENSG00000012061:ENST00000013807:exon8:c.C964T:p.R322C, 322 R/C 20,0 16,0 0,0,145 0,1,490 0,0,145 0,1,466 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0377 99 chr19:33464113:33464113:-:C:indel 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr19 33464113 33464113 - C indel frameshift insertion C19orf40:NM_152266:exon2:c.11_12insC:p.C4fs, frameshift insertion C19orf40 frameshift_variant,feature_elongation frameshift insertion ENSG00000131944 PASS TRUE TRUE TRUE TRUE TRUE -3.8 0.00157233 ENSG00000131944:ENST00000254262:exon2:c.11_12insC:p.N4fs,ENSG00000131944:ENST00000590281:exon2:c.11_12insC:p.N4fs,ENSG00000131944:ENST00000588258:exon2:c.11_12insC:p.N4fs, 4 - 44,0 41,0 0,0,145 0,2,489 0,0,145 0,2,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0065,AOGC-02-0069 99,99 chr1:28218633:28218633:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr1 28218633 28218633 G A snp UTR3 RPA2 UTR3 RPA2 3_prime_UTR_variant UTR3 ENSG00000117748 PASS FALSE TRUE TRUE TRUE TRUE 4.52 0.000784929 ENSG00000117748 - - 21,0 24,0 0,0,146 0,1,490 0,0,146 0,1,489 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0462 99 chr1:28233491:28233491:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr1 28233491 28233491 A G snp nonsynonymous SNV RPA2:NM_001297558:exon4:c.T305C:p.I102T,RPA2:NM_002946:exon4:c.T281C:p.I94T, nonsynonymous SNV RPA2 missense_variant nonsynonymous SNV ENSG00000117748 PASS FALSE TRUE TRUE TRUE TRUE 5.83 0.000784929 ENSG00000117748:ENST00000373912:exon4:c.T281C:p.I94T,ENSG00000117748:ENST00000373909:exon4:c.T305C:p.I102T,ENSG00000117748:ENST00000313433:exon3:c.T545C:p.I182T,ENSG00000117748:ENST00000444045:exon4:c.T293C:p.I98T, 182 I/T 21,0 20,0 0,0,146 0,1,490 0,0,146 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0161 99 chr1:28240648:28240648:C:T:snp 0.388498361735038 -0.122222222222221 0.141732593760593 0.00704225352112676 0.00704225352112676 1 1 0 chr1 28240648 28240648 C T snp nonsynonymous SNV RPA2:NM_001297558:exon2:c.G67A:p.G23R,RPA2:NM_002946:exon2:c.G43A:p.G15R, nonsynonymous SNV RPA2 missense_variant nonsynonymous SNV ENSG00000117748 PASS FALSE FALSE FALSE TRUE TRUE 2.57 0.00717703 ENSG00000117748:ENST00000373912:exon2:c.G43A:p.G15R,ENSG00000117748:ENST00000373909:exon2:c.G67A:p.G23R,ENSG00000117748:ENST00000313433:exon1:c.G307A:p.G103R,ENSG00000117748:ENST00000444045:exon2:c.G55A:p.G19R, 103 G/R 14,0 8,0 0,1,145 0,8,473 0,1,145 0,7,419 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2835-03B-01W-0728-08 99 AOGC-02-0015,AOGC-02-0064,AOGC-02-0297,AOGC-02-0430,AOGC-03-0091,AOGC-03-0117,AOGC-03-0152,AOGC-08-0237 99,99,85,86,99,99,99,72 chr1:28241179:28241179:A:G:snp 0.866515946988662 -0.0318611987381696 0.189553423814011 0.00391236306729264 0.00391236306729264 1 1 0 chr1 28241179 28241179 A G snp UTR5 RPA2 UTR5 RPA2 5_prime_UTR_variant UTR5 ENSG00000117748 PASS FALSE FALSE TRUE TRUE TRUE 3.75 0.00410509 ENSG00000117748 - - 24,0 10,0 0,1,145 0,4,459 0,1,144 0,3,393 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2804-03B-01W-0728-08 99 AOGC-02-0112,AOGC-02-0162,AOGC-02-0478,AOGC-03-0124 99,99,69,99 chr22:29083962:29083962:G:C:snp 0.0664550513228258 -0.235668789808916 0.128405935709664 0.00860719874804382 0.00860719874804382 1 1 0 chr22 29083962 29083962 G C snp nonsynonymous SNV CHEK2:NM_007194:exon15:c.C1555G:p.R519G,CHEK2:NM_001005735:exon16:c.C1684G:p.R562G,CHEK2:NM_001257387:exon16:c.C892G:p.R298G,CHEK2:NM_145862:exon14:c.C1468G:p.R490G, nonsynonymous SNV CHEK2 missense_variant nonsynonymous SNV ENSG00000183765 PASS FALSE TRUE TRUE TRUE TRUE 3.66 0.00925926 ENSG00000183765:ENST00000544772:exon16:c.C892G:p.R298G,ENSG00000183765:ENST00000382578:exon13:c.C1282G:p.R428G,ENSG00000183765:ENST00000403642:exon12:c.C1282G:p.R428G,ENSG00000183765:ENST00000382580:exon16:c.C1684G:p.R562G,ENSG00000183765:ENST00000405598:exon16:c.C1555G:p.R519G,ENSG00000183765:ENST00000328354:exon15:c.C1555G:p.R519G,ENSG00000183765:ENST00000404276:exon14:c.C1555G:p.R519G,ENSG00000183765:ENST00000382565:exon5:c.C415G:p.R139G,ENSG00000183765:ENST00000402731:exon13:c.C1468G:p.R490G,ENSG00000183765:ENST00000348295:exon14:c.C1468G:p.R490G, 298 R/G 22,0 22,0 0,0,145 0,11,438 0,0,144 0,10,418 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0030,AOGC-02-0099,AOGC-02-0138,AOGC-02-0274,AOGC-02-0306,AOGC-02-0369,AOGC-02-0386,AOGC-03-0091,AOGC-08-0048,AOGC-08-0081,AOGC-08-0159 57,15,22,47,87,40,39,25,55,22,69 chr22:29085140:29085140:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr22 29085140 29085140 G A snp nonsynonymous SNV CHEK2:NM_007194:exon14:c.C1525T:p.P509S,CHEK2:NM_001005735:exon15:c.C1654T:p.P552S,CHEK2:NM_001257387:exon15:c.C862T:p.P288S,CHEK2:NM_145862:exon13:c.C1438T:p.P480S, nonsynonymous SNV CHEK2 missense_variant nonsynonymous SNV ENSG00000183765 PASS TRUE TRUE TRUE TRUE TRUE -2.34 0.000840336 ENSG00000183765:ENST00000544772:exon15:c.C862T:p.P288S,ENSG00000183765:ENST00000382578:exon12:c.C1252T:p.P418S,ENSG00000183765:ENST00000403642:exon11:c.C1252T:p.P418S,ENSG00000183765:ENST00000382580:exon15:c.C1654T:p.P552S,ENSG00000183765:ENST00000405598:exon15:c.C1525T:p.P509S,ENSG00000183765:ENST00000328354:exon14:c.C1525T:p.P509S,ENSG00000183765:ENST00000404276:exon13:c.C1525T:p.P509S,ENSG00000183765:ENST00000382565:exon4:c.C385T:p.P129S,ENSG00000183765:ENST00000402731:exon12:c.C1438T:p.P480S,ENSG00000183765:ENST00000348295:exon13:c.C1438T:p.P480S, 288 P/S 20,0 26,0 0,0,145 0,1,449 0,0,145 0,1,442 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0150 99 chr22:29091743:29091743:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr22 29091743 29091743 T C snp nonsynonymous SNV CHEK2:NM_007194:exon11:c.A1214G:p.N405S,CHEK2:NM_001005735:exon12:c.A1343G:p.N448S,CHEK2:NM_001257387:exon12:c.A551G:p.N184S,CHEK2:NM_145862:exon10:c.A1127G:p.N376S, nonsynonymous SNV CHEK2 missense_variant nonsynonymous SNV ENSG00000183765 PASS FALSE TRUE TRUE TRUE TRUE 3.43 0.000784929 ENSG00000183765:ENST00000544772:exon12:c.A551G:p.N184S,ENSG00000183765:ENST00000382578:exon9:c.A941G:p.N314S,ENSG00000183765:ENST00000403642:exon8:c.A941G:p.N314S,ENSG00000183765:ENST00000382580:exon12:c.A1343G:p.N448S,ENSG00000183765:ENST00000405598:exon12:c.A1214G:p.N405S,ENSG00000183765:ENST00000328354:exon11:c.A1214G:p.N405S,ENSG00000183765:ENST00000404276:exon10:c.A1214G:p.N405S,ENSG00000183765:ENST00000402731:exon9:c.A1127G:p.N376S,ENSG00000183765:ENST00000348295:exon10:c.A1127G:p.N376S, 184 N/S 23,0 24,0 0,0,146 0,1,490 0,0,145 0,1,474 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0504 99 chr22:29095844:29095844:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr22 29095844 29095844 C T snp synonymous SNV CHEK2:NM_007194:exon9:c.G990A:p.Q330Q,CHEK2:NM_001005735:exon10:c.G1119A:p.Q373Q,CHEK2:NM_001257387:exon10:c.G327A:p.Q109Q,CHEK2:NM_145862:exon9:c.G990A:p.Q330Q, synonymous SNV CHEK2 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000183765 PASS FALSE TRUE TRUE TRUE TRUE 4.63 0.000787402 ENSG00000183765:ENST00000544772:exon10:c.G327A:p.Q109Q,ENSG00000183765:ENST00000382578:exon7:c.G717A:p.Q239Q,ENSG00000183765:ENST00000403642:exon6:c.G717A:p.Q239Q,ENSG00000183765:ENST00000382580:exon10:c.G1119A:p.Q373Q,ENSG00000183765:ENST00000405598:exon10:c.G990A:p.Q330Q,ENSG00000183765:ENST00000425190:exon8:c.G327A:p.Q109Q,ENSG00000183765:ENST00000328354:exon9:c.G990A:p.Q330Q,ENSG00000183765:ENST00000404276:exon8:c.G990A:p.Q330Q,ENSG00000183765:ENST00000447421:exon7:c.G789A:p.Q263Q,ENSG00000183765:ENST00000402731:exon8:c.G990A:p.Q330Q,ENSG00000183765:ENST00000348295:exon9:c.G990A:p.Q330Q, - - 22,0 24,0 0,0,145 0,1,489 0,0,145 0,1,486 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0388 99 chr22:29095923:29095923:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr22 29095923 29095923 A G snp nonsynonymous SNV CHEK2:NM_007194:exon9:c.T911C:p.M304T,CHEK2:NM_001005735:exon10:c.T1040C:p.M347T,CHEK2:NM_001257387:exon10:c.T248C:p.M83T,CHEK2:NM_145862:exon9:c.T911C:p.M304T, nonsynonymous SNV CHEK2 missense_variant,splice_region_variant nonsynonymous SNV ENSG00000183765 PASS FALSE TRUE TRUE TRUE TRUE 5.67 0.000786164 ENSG00000183765:ENST00000544772:exon10:c.T248C:p.M83T,ENSG00000183765:ENST00000382578:exon7:c.T638C:p.M213T,ENSG00000183765:ENST00000403642:exon6:c.T638C:p.M213T,ENSG00000183765:ENST00000382580:exon10:c.T1040C:p.M347T,ENSG00000183765:ENST00000405598:exon10:c.T911C:p.M304T,ENSG00000183765:ENST00000425190:exon8:c.T248C:p.M83T,ENSG00000183765:ENST00000328354:exon9:c.T911C:p.M304T,ENSG00000183765:ENST00000404276:exon8:c.T911C:p.M304T,ENSG00000183765:ENST00000447421:exon7:c.T710C:p.M237T,ENSG00000183765:ENST00000402731:exon8:c.T911C:p.M304T,ENSG00000183765:ENST00000348295:exon9:c.T911C:p.M304T, 83 M/T 22,0 24,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0284 99 chr22:29107954:29107954:T:A:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr22 29107954 29107954 T A snp nonsynonymous SNV CHEK2:NM_007194:exon6:c.A735T:p.K245N,CHEK2:NM_001005735:exon7:c.A864T:p.K288N,CHEK2:NM_001257387:exon7:c.A72T:p.K24N,CHEK2:NM_145862:exon6:c.A735T:p.K245N, nonsynonymous SNV CHEK2 missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000183765 PASS TRUE TRUE TRUE TRUE TRUE 5.27 0.0015748 ENSG00000183765:ENST00000544772:exon7:c.A72T:p.K24N,ENSG00000183765:ENST00000382578:exon4:c.A462T:p.K154N,ENSG00000183765:ENST00000439200:exon7:c.A828T:p.K276N,ENSG00000183765:ENST00000403642:exon3:c.A462T:p.K154N,ENSG00000183765:ENST00000382580:exon7:c.A864T:p.K288N,ENSG00000183765:ENST00000382566:exon6:c.A735T:p.K245N,ENSG00000183765:ENST00000405598:exon7:c.A735T:p.K245N,ENSG00000183765:ENST00000425190:exon5:c.A72T:p.K24N,ENSG00000183765:ENST00000328354:exon6:c.A735T:p.K245N,ENSG00000183765:ENST00000404276:exon5:c.A735T:p.K245N,ENSG00000183765:ENST00000433728:exon5:c.A735T:p.K245N,ENSG00000183765:ENST00000447421:exon4:c.A534T:p.K178N,ENSG00000183765:ENST00000402731:exon5:c.A735T:p.K245N,ENSG00000183765:ENST00000348295:exon6:c.A735T:p.K245N, 245 K/N 30,0 20,0 0,0,145 0,2,488 0,0,145 0,2,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0346,AOGC-02-0462 19,99 chr22:29115415:29115415:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr22 29115415 29115415 T C snp synonymous SNV CHEK2:NM_007194:exon5:c.A651G:p.R217R,CHEK2:NM_001005735:exon6:c.A780G:p.R260R,CHEK2:NM_145862:exon5:c.A651G:p.R217R, synonymous SNV CHEK2 5_prime_UTR_variant synonymous SNV ENSG00000183765 PASS FALSE TRUE TRUE TRUE TRUE 5.51 0.000789889 ENSG00000183765:ENST00000382578:exon3:c.A378G:p.R126R,ENSG00000183765:ENST00000439200:exon6:c.A744G:p.R248R,ENSG00000183765:ENST00000403642:exon2:c.A378G:p.R126R,ENSG00000183765:ENST00000382580:exon6:c.A780G:p.R260R,ENSG00000183765:ENST00000382566:exon5:c.A651G:p.R217R,ENSG00000183765:ENST00000405598:exon6:c.A651G:p.R217R,ENSG00000183765:ENST00000328354:exon5:c.A651G:p.R217R,ENSG00000183765:ENST00000404276:exon4:c.A651G:p.R217R,ENSG00000183765:ENST00000433728:exon4:c.A651G:p.R217R,ENSG00000183765:ENST00000402731:exon4:c.A651G:p.R217R,ENSG00000183765:ENST00000348295:exon5:c.A651G:p.R217R, - - 7,0 2,0 0,0,145 0,1,487 0,0,126 0,1,449 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0251 99 chr22:29121019:29121019:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr22 29121019 29121019 G A snp nonsynonymous SNV CHEK2:NM_007194:exon4:c.C538T:p.R180C,CHEK2:NM_001005735:exon5:c.C667T:p.R223C,CHEK2:NM_145862:exon4:c.C538T:p.R180C, nonsynonymous SNV CHEK2 missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000183765 PASS FALSE FALSE TRUE TRUE TRUE 5.87 0.000784929 ENSG00000183765:ENST00000417588:exon3:c.C538T:p.R180C,ENSG00000183765:ENST00000416671:exon4:c.C538T:p.R180C,ENSG00000183765:ENST00000439200:exon5:c.C631T:p.R211C,ENSG00000183765:ENST00000382580:exon5:c.C667T:p.R223C,ENSG00000183765:ENST00000382566:exon4:c.C538T:p.R180C,ENSG00000183765:ENST00000405598:exon5:c.C538T:p.R180C,ENSG00000183765:ENST00000439346:exon2:c.C100T:p.R34C,ENSG00000183765:ENST00000328354:exon4:c.C538T:p.R180C,ENSG00000183765:ENST00000404276:exon3:c.C538T:p.R180C,ENSG00000183765:ENST00000433728:exon3:c.C538T:p.R180C,ENSG00000183765:ENST00000402731:exon3:c.C538T:p.R180C,ENSG00000183765:ENST00000348295:exon4:c.C538T:p.R180C, 34 R/C 32,0 23,0 0,1,145 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2856-03A-01W-0726-08 99 chr22:29121360:29121360:A:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr22 29121360 29121360 A T snp splicing CHEK2(NM_145862:exon4:c.320-5T>A,NM_007194:exon4:c.320-5T>A,NM_001005735:exon5:c.449-5T>A) splicing CHEK2 splice_region_variant,intron_variant,NMD_transcript_variant splicing ENSG00000183765 PASS FALSE FALSE TRUE TRUE TRUE 4.65 0.000786164 ENSG00000183765(ENST00000382566:exon4:c.320-5T>A,ENST00000348295:exon4:c.320-5T>A,ENST00000416671:exon4:c.320-5T>A,ENST00000328354:exon4:c.320-5T>A,ENST00000404276:exon3:c.320-5T>A,ENST00000405598:exon5:c.320-5T>A,ENST00000382580:exon5:c.449-5T>A,ENST00000433728:exon3:c.320-5T>A,ENST00000417588:exon3:c.320-5T>A,ENST00000448511:exon3:c.320-5T>A,ENST00000402731:exon3:c.320-5T>A,ENST00000447421:exon3:c.320-5T>A,ENST00000433028:exon4:c.320-5T>A,ENST00000439200:exon5:c.413-5T>A,ENST00000454252:exon6:c.438-5T>A,ENST00000398017:exon6:c.350-5T>A) - - 32,0 23,0 0,1,144 0,0,491 0,1,144 0,0,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2867-03B-01W-0728-08 99 chr22:29091857:29091857:G:-:indel 0.369333103048797 -0.155055002619172 0.172720267671242 0.00312989045383412 0.00312989045383412 1 1 0 chr22 29091857 29091857 G - indel frameshift deletion CHEK2:NM_007194:exon11:c.1100delC:p.T367fs,CHEK2:NM_001005735:exon12:c.1229delC:p.T410fs,CHEK2:NM_001257387:exon12:c.437delC:p.T146fs,CHEK2:NM_145862:exon10:c.1013delC:p.T338fs, frameshift deletion CHEK2 frameshift_variant,feature_truncation frameshift deletion ENSG00000183765 PASS FALSE FALSE TRUE TRUE TRUE 5.89 0.00314961 ENSG00000183765:ENST00000544772:exon12:c.437delC:p.T146fs,ENSG00000183765:ENST00000382578:exon9:c.827delC:p.T276fs,ENSG00000183765:ENST00000403642:exon8:c.827delC:p.T276fs,ENSG00000183765:ENST00000382580:exon12:c.1229delC:p.T410fs,ENSG00000183765:ENST00000405598:exon12:c.1100delC:p.T367fs,ENSG00000183765:ENST00000328354:exon11:c.1100delC:p.T367fs,ENSG00000183765:ENST00000404276:exon10:c.1100delC:p.T367fs,ENSG00000183765:ENST00000402731:exon9:c.1013delC:p.T338fs,ENSG00000183765:ENST00000348295:exon10:c.1013delC:p.T338fs, 146 - 26,0 24,0 0,0,146 1,2,486 0,0,145 1,1,430 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 0.00347624565469293 1 0 1 AOGC-02-0441,AOGC-02-0471,AOGC-08-0054 15,99,94 chr2:58388728:58388728:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr2 58388728 58388728 C T snp nonsynonymous SNV FANCL:NM_001114636:exon12:c.G964A:p.G322S,FANCL:NM_018062:exon12:c.G949A:p.G317S, nonsynonymous SNV FANCL missense_variant nonsynonymous SNV ENSG00000115392 PASS TRUE TRUE TRUE TRUE TRUE 5.91 0.000786164 ENSG00000115392:ENST00000233741:exon12:c.G949A:p.G317S,ENSG00000115392:ENST00000449070:exon9:c.G772A:p.G258S,ENSG00000115392:ENST00000403295:exon11:c.G865A:p.G289S,ENSG00000115392:ENST00000403676:exon8:c.G598A:p.G200S,ENSG00000115392:ENST00000402135:exon12:c.G964A:p.G322S, 317 G/S 30,0 23,0 0,1,145 0,0,490 0,1,145 0,0,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2834-03B-01W-0728-08 99 chr2:58390231:58390231:T:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr2 58390231 58390231 T A snp intronic FANCL intronic FANCL non_coding_exon_variant,nc_transcript_variant intronic ENSG00000115392 PASS FALSE FALSE TRUE TRUE TRUE 3.67 0.000823723 ENSG00000115392 - - 22,0 8,0 0,0,146 0,1,460 0,0,144 0,1,449 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0060 99 chr2:58392880:58392880:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr2 58392880 58392880 T C snp nonsynonymous SNV FANCL:NM_001114636:exon8:c.A685G:p.T229A,FANCL:NM_018062:exon8:c.A670G:p.T224A, nonsynonymous SNV FANCL missense_variant nonsynonymous SNV ENSG00000115392 PASS FALSE FALSE TRUE TRUE TRUE 5.73 0.000786164 ENSG00000115392:ENST00000233741:exon8:c.A670G:p.T224A,ENSG00000115392:ENST00000449070:exon5:c.A493G:p.T165A,ENSG00000115392:ENST00000446381:exon2:c.A226G:p.T76A,ENSG00000115392:ENST00000403295:exon8:c.A670G:p.T224A,ENSG00000115392:ENST00000403676:exon4:c.A319G:p.T107A,ENSG00000115392:ENST00000402135:exon8:c.A685G:p.T229A,ENSG00000115392:ENST00000417361:exon4:c.A334G:p.T112A, 224 T/A 26,0 25,0 0,0,146 0,1,489 0,0,146 0,1,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0136 99 chr2:58393004:58393004:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr2 58393004 58393004 G A snp synonymous SNV FANCL:NM_001114636:exon8:c.C561T:p.S187S,FANCL:NM_018062:exon8:c.C546T:p.S182S, nonsynonymous SNV FANCL missense_variant synonymous SNV ENSG00000115392 PASS FALSE FALSE TRUE TRUE TRUE 1.12 0.000784929 ENSG00000115392:ENST00000540646:exon6:c.C380T:p.P127L, 127 P/L 26,0 25,0 0,0,147 0,1,489 0,0,145 0,1,465 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0333 99 chr2:58456962:58456962:C:G:snp 0.675730396862748 0.102201257861636 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr2 58456962 58456962 C G snp nonsynonymous SNV FANCL:NM_001114636:exon3:c.G203C:p.R68P,FANCL:NM_018062:exon3:c.G203C:p.R68P, nonsynonymous SNV FANCL missense_variant nonsynonymous SNV ENSG00000115392 PASS FALSE FALSE TRUE TRUE TRUE 2.99 0.00236967 ENSG00000115392:ENST00000233741:exon3:c.G203C:p.R68P,ENSG00000115392:ENST00000540646:exon3:c.G203C:p.R68P,ENSG00000115392:ENST00000403295:exon3:c.G203C:p.R68P,ENSG00000115392:ENST00000402135:exon3:c.G203C:p.R68P, 68 R/P 22,0 21,0 0,1,145 0,2,485 0,1,145 0,2,454 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2921-03A-01W-0755-09 99 AOGC-02-0283,AOGC-08-0046 99,99 chr2:58459232:58459232:G:A:snp 0.575977326218678 -0.0897377938517171 0.160455166401833 0.0054773082942097 0.0054773082942097 1 1 0 chr2 58459232 58459232 G A snp nonsynonymous SNV FANCL:NM_001114636:exon2:c.C112T:p.L38F,FANCL:NM_018062:exon2:c.C112T:p.L38F, nonsynonymous SNV FANCL missense_variant nonsynonymous SNV ENSG00000115392 PASS FALSE FALSE FALSE TRUE TRUE 4.06 0.00550314 ENSG00000115392:ENST00000233741:exon2:c.C112T:p.L38F,ENSG00000115392:ENST00000540646:exon2:c.C112T:p.L38F,ENSG00000115392:ENST00000403295:exon2:c.C112T:p.L38F,ENSG00000115392:ENST00000402135:exon2:c.C112T:p.L38F, 38 L/F 23,0 25,0 0,1,145 0,6,484 0,1,145 0,6,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2808-03D-01W-0755-09 99 AOGC-02-0009,AOGC-02-0041,AOGC-02-0314,AOGC-02-0367,AOGC-03-0035,AOGC-14-0064 99,99,99,99,99,99 chr2:58459236:58459236:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr2 58459236 58459236 G C snp nonsynonymous SNV FANCL:NM_001114636:exon2:c.C108G:p.F36L,FANCL:NM_018062:exon2:c.C108G:p.F36L, nonsynonymous SNV FANCL missense_variant nonsynonymous SNV ENSG00000115392 PASS FALSE TRUE TRUE TRUE TRUE 3.24 0.000786164 ENSG00000115392:ENST00000233741:exon2:c.C108G:p.F36L,ENSG00000115392:ENST00000540646:exon2:c.C108G:p.F36L,ENSG00000115392:ENST00000403295:exon2:c.C108G:p.F36L,ENSG00000115392:ENST00000402135:exon2:c.C108G:p.F36L, 36 F/L 23,0 25,0 0,0,146 0,1,489 0,0,146 0,1,484 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0280 99 chr2:215593543:215593543:G:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr2 215593543 215593543 G C snp nonsynonymous SNV BARD1:NM_001282548:exon6:c.C781G:p.R261G,BARD1:NM_000465:exon11:c.C2191G:p.R731G,BARD1:NM_001282549:exon5:c.C652G:p.R218G,BARD1:NM_001282545:exon7:c.C838G:p.R280G,BARD1:NM_001282543:exon10:c.C2134G:p.R712G, nonsynonymous SNV BARD1 missense_variant nonsynonymous SNV ENSG00000138376 PASS FALSE FALSE FALSE TRUE TRUE 5.81 0.000784929 ENSG00000138376:ENST00000432456:exon3:c.C304G:p.R102G,ENSG00000138376:ENST00000260947:exon11:c.C2191G:p.R731G, 731 R/G 29,0 20,0 0,1,145 0,0,491 0,1,145 0,0,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2891-03A-01W-0733-08 99 chr2:215593573:215593573:C:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr2 215593573 215593573 C A snp nonsynonymous SNV BARD1:NM_001282548:exon6:c.G751T:p.A251S,BARD1:NM_000465:exon11:c.G2161T:p.A721S,BARD1:NM_001282549:exon5:c.G622T:p.A208S,BARD1:NM_001282545:exon7:c.G808T:p.A270S,BARD1:NM_001282543:exon10:c.G2104T:p.A702S, nonsynonymous SNV BARD1 missense_variant nonsynonymous SNV ENSG00000138376 PASS FALSE FALSE TRUE TRUE TRUE 3.8 0.000784929 ENSG00000138376:ENST00000432456:exon3:c.G274T:p.A92S,ENSG00000138376:ENST00000260947:exon11:c.G2161T:p.A721S, 721 A/S 29,0 20,0 0,0,146 0,1,490 0,0,146 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0457 99 chr2:215595159:215595159:T:C:snp 0.733167316798394 0.0547016274864384 0.160455166401833 0.0054773082942097 0.0054773082942097 1 1 0 chr2 215595159 215595159 T C snp synonymous SNV BARD1:NM_001282548:exon5:c.A567G:p.R189R,BARD1:NM_000465:exon10:c.A1977G:p.R659R,BARD1:NM_001282549:exon4:c.A438G:p.R146R,BARD1:NM_001282545:exon6:c.A624G:p.R208R,BARD1:NM_001282543:exon9:c.A1920G:p.R640R, synonymous SNV BARD1 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000138376 PASS FALSE FALSE FALSE TRUE TRUE 4.62 0.00549451 ENSG00000138376:ENST00000432456:exon2:c.A90G:p.R30R,ENSG00000138376:ENST00000421162:exon6:c.A624G:p.R208R,ENSG00000138376:ENST00000449967:exon9:c.A1545G:p.R515R,ENSG00000138376:ENST00000260947:exon10:c.A1977G:p.R659R, - - 28,0 21,0 0,2,144 0,5,486 0,2,144 0,5,483 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2896-03A-01W-0733-08,TCGA-AB-2942-03A-01W-0733-08 99,99 AOGC-02-0013,AOGC-02-0389,AOGC-03-0079,AOGC-08-0283,AOGC-14-0154 99,99,99,99,78 chr2:215632322:215632322:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr2 215632322 215632322 C T snp synonymous SNV BARD1:NM_000465:exon6:c.G1452A:p.K484K,BARD1:NM_001282543:exon5:c.G1395A:p.K465K, synonymous SNV BARD1 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000138376 PASS FALSE TRUE TRUE TRUE TRUE 2.43 0.000783699 ENSG00000138376:ENST00000449967:exon5:c.G1020A:p.K340K,ENSG00000138376:ENST00000260947:exon6:c.G1452A:p.K484K, - - 31,0 26,0 0,0,147 0,1,490 0,0,146 0,1,487 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0141 99 chr2:58459321:58459325:AAAGA:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr2 58459321 58459325 AAAGA - indel intronic FANCL intronic FANCL intron_variant,feature_truncation intronic ENSG00000115392 PASS FALSE TRUE TRUE TRUE TRUE 2.82 0.000789889 ENSG00000115392 - - 9,0 3,0 0,0,144 0,1,488 0,0,129 0,1,464 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0187 99 chr3:10070369:10070369:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10070369 10070369 T C snp nonsynonymous SNV FANCD2:NM_033084:exon2:c.T28C:p.S10P,FANCD2:NM_001018115:exon2:c.T28C:p.S10P, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS FALSE TRUE TRUE TRUE TRUE 1.47 0.000791139 ENSG00000144554:ENST00000287647:exon2:c.T28C:p.S10P,ENSG00000144554:ENST00000383806:exon2:c.T28C:p.S10P,ENSG00000144554:ENST00000435522:exon2:c.T28C:p.S10P,ENSG00000144554:ENST00000383807:exon2:c.T28C:p.S10P,ENSG00000144554:ENST00000419585:exon2:c.T28C:p.S10P,ENSG00000144554:ENST00000431693:exon1:c.T28C:p.S10P, 10 S/P 22,0 21,0 0,0,146 0,1,485 0,0,146 0,1,447 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0283 99 chr3:10074529:10074529:A:C:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr3 10074529 10074529 A C snp nonsynonymous SNV FANCD2:NM_033084:exon3:c.A78C:p.Q26H,FANCD2:NM_001018115:exon3:c.A78C:p.Q26H, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS FALSE TRUE TRUE TRUE TRUE -1.69 0.00157233 ENSG00000144554:ENST00000287647:exon3:c.A78C:p.Q26H,ENSG00000144554:ENST00000383806:exon3:c.A78C:p.Q26H,ENSG00000144554:ENST00000383807:exon3:c.A78C:p.Q26H,ENSG00000144554:ENST00000419585:exon3:c.A78C:p.Q26H,ENSG00000144554:ENST00000431693:exon2:c.A78C:p.Q26H, 26 Q/H 27,0 26,0 0,1,145 0,1,489 0,1,145 0,1,448 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2912-03A-01W-0732-08 99 AOGC-03-0076 99 chr3:10077031:10077031:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10077031 10077031 G A snp intronic FANCD2 intronic FANCD2 intron_variant intronic ENSG00000144554 PASS FALSE FALSE TRUE TRUE TRUE 2.67 0.000786164 ENSG00000144554 - - 8,0 3,0 0,0,145 0,1,490 0,0,137 0,1,479 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0165 99 chr3:10077958:10077958:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10077958 10077958 T C snp intronic FANCD2 intronic FANCD2 intron_variant intronic ENSG00000144554 PASS TRUE TRUE TRUE TRUE TRUE 5.38 0.000787402 ENSG00000144554 - - 30,0 25,0 0,1,146 0,0,488 0,1,146 0,0,455 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2855-03B-01W-0728-08 99 chr3:10081386:10081386:A:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10081386 10081386 A T snp intronic FANCD2 intronic FANCD2 intron_variant intronic ENSG00000144554 PASS FALSE TRUE TRUE TRUE TRUE 2.3 0.000786164 ENSG00000144554 - - 30,0 21,0 0,1,144 0,0,491 0,1,144 0,0,480 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2852-03A-01W-0726-08 99 chr3:10081411:10081411:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10081411 10081411 A G snp nonsynonymous SNV FANCD2:NM_033084:exon9:c.A577G:p.T193A,FANCD2:NM_001018115:exon9:c.A577G:p.T193A, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS FALSE FALSE TRUE TRUE TRUE 5.16 0.000786164 ENSG00000144554:ENST00000287647:exon9:c.A577G:p.T193A,ENSG00000144554:ENST00000383806:exon9:c.A577G:p.T193A,ENSG00000144554:ENST00000383807:exon9:c.A577G:p.T193A,ENSG00000144554:ENST00000419585:exon9:c.A577G:p.T193A,ENSG00000144554:ENST00000431693:exon8:c.A577G:p.T193A, 193 T/A 30,0 21,0 0,0,145 0,1,490 0,0,145 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0098 99 chr3:10084276:10084276:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10084276 10084276 A G snp nonsynonymous SNV FANCD2:NM_033084:exon11:c.A817G:p.I273V,FANCD2:NM_001018115:exon11:c.A817G:p.I273V, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS FALSE TRUE TRUE TRUE TRUE 2.76 0.000784929 ENSG00000144554:ENST00000287647:exon11:c.A817G:p.I273V,ENSG00000144554:ENST00000383806:exon11:c.A817G:p.I273V,ENSG00000144554:ENST00000383807:exon11:c.A817G:p.I273V,ENSG00000144554:ENST00000419585:exon11:c.A817G:p.I273V, 273 I/V 25,0 22,0 0,0,146 0,1,490 0,0,146 0,1,484 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0001 99 chr3:10085556:10085556:T:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10085556 10085556 T G snp intronic FANCD2 intronic FANCD2 splice_region_variant,intron_variant intronic ENSG00000144554 PASS FALSE TRUE TRUE TRUE TRUE 2.25 0.000787402 ENSG00000144554 - - 31,0 14,0 0,1,145 0,0,489 0,1,145 0,0,450 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2855-03B-01W-0728-08 99 chr3:10094070:10094070:G:C:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr3 10094070 10094070 G C snp splicing FANCD2(NM_033084:exon18:c.1546-1G>C,NM_001018115:exon18:c.1546-1G>C) splicing FANCD2 splice_acceptor_variant splicing ENSG00000144554 PASS FALSE FALSE TRUE TRUE TRUE 5.55 0.00156986 ENSG00000144554(ENST00000287647:exon18:c.1546-1G>C,ENST00000383806:exon18:c.1546-1G>C,ENST00000383807:exon18:c.1546-1G>C,ENST00000419585:exon18:c.1546-1G>C,ENST00000421731:exon2:c.45-1G>C) - - 42,0 21,0 0,0,146 0,2,489 0,0,146 0,2,464 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0285,AOGC-14-0081 99,99 chr3:10094177:10094177:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10094177 10094177 T C snp nonsynonymous SNV FANCD2:NM_033084:exon18:c.T1652C:p.I551T,FANCD2:NM_001018115:exon18:c.T1652C:p.I551T, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS TRUE TRUE TRUE TRUE TRUE 4.33 0.000784929 ENSG00000144554:ENST00000287647:exon18:c.T1652C:p.I551T,ENSG00000144554:ENST00000383806:exon18:c.T1652C:p.I551T,ENSG00000144554:ENST00000383807:exon18:c.T1652C:p.I551T,ENSG00000144554:ENST00000419585:exon18:c.T1652C:p.I551T, 551 I/T 42,0 21,0 0,1,145 0,0,491 0,1,145 0,0,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2932-03A-01W-0745-08 99 chr3:10103845:10103845:C:T:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr3 10103845 10103845 C T snp nonsynonymous SNV FANCD2:NM_033084:exon20:c.C1777T:p.P593S,FANCD2:NM_001018115:exon20:c.C1777T:p.P593S, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS FALSE FALSE TRUE TRUE TRUE 2.2 0.0015674 ENSG00000144554:ENST00000287647:exon20:c.C1777T:p.P593S,ENSG00000144554:ENST00000383806:exon20:c.C1777T:p.P593S,ENSG00000144554:ENST00000383807:exon20:c.C1777T:p.P593S,ENSG00000144554:ENST00000419585:exon20:c.C1777T:p.P593S, 593 P/S 20,0 21,0 0,1,146 0,1,490 0,1,145 0,1,478 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2895-03A-01W-0733-08 99 AOGC-01-0003 99 chr3:10106472:10106472:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10106472 10106472 G A snp nonsynonymous SNV FANCD2:NM_033084:exon23:c.G2081A:p.G694E,FANCD2:NM_001018115:exon23:c.G2081A:p.G694E, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS TRUE TRUE TRUE TRUE TRUE 4.76 0.000783699 ENSG00000144554:ENST00000287647:exon23:c.G2081A:p.G694E,ENSG00000144554:ENST00000383806:exon23:c.G2081A:p.G694E,ENSG00000144554:ENST00000383807:exon23:c.G2081A:p.G694E,ENSG00000144554:ENST00000419585:exon23:c.G2081A:p.G694E, 694 G/E 24,0 23,0 0,1,146 0,0,491 0,1,145 0,0,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2819-03B-01W-0728-08 99 chr3:10115047:10115047:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10115047 10115047 G A snp splicing FANCD2(NM_033084:exon28:c.2715+1G>A,NM_001018115:exon28:c.2715+1G>A) splicing FANCD2 splice_donor_variant splicing ENSG00000144554 PASS FALSE FALSE TRUE TRUE TRUE 5.83 0.000783699 ENSG00000144554(ENST00000287647:exon28:c.2715+1G>A,ENST00000383806:exon28:c.2715+1G>A,ENST00000383807:exon28:c.2715+1G>A,ENST00000419585:exon28:c.2715+1G>A,ENST00000421731:exon12:c.1214+1G>A) - - 37,0 22,0 0,0,147 0,1,490 0,0,146 0,1,473 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0208 99 chr3:10132041:10132041:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10132041 10132041 A G snp nonsynonymous SNV FANCD2:NM_033084:exon37:c.A3749G:p.E1250G,FANCD2:NM_001018115:exon37:c.A3749G:p.E1250G, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS TRUE TRUE TRUE TRUE TRUE 3.22 0.000784929 ENSG00000144554:ENST00000287647:exon37:c.A3749G:p.E1250G,ENSG00000144554:ENST00000383807:exon37:c.A3749G:p.E1250G,ENSG00000144554:ENST00000419585:exon37:c.A3749G:p.E1250G, 1250 E/G 22,0 7,0 0,0,146 0,1,490 0,0,146 0,1,481 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0247 96 chr3:10138023:10138023:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10138023 10138023 C T snp nonsynonymous SNV FANCD2:NM_033084:exon42:c.C4052T:p.T1351M,FANCD2:NM_001018115:exon42:c.C4052T:p.T1351M, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS FALSE TRUE TRUE TRUE TRUE -4.3 0.000784929 ENSG00000144554:ENST00000287647:exon42:c.C4052T:p.T1351M,ENSG00000144554:ENST00000383807:exon42:c.C4052T:p.T1351M,ENSG00000144554:ENST00000419585:exon42:c.C4052T:p.T1351M, 1351 T/M 20,0 21,0 0,0,146 0,1,490 0,0,146 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0069 99 chr3:10142942:10142942:A:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 10142942 10142942 A C snp nonsynonymous SNV FANCD2:NM_001018115:exon44:c.A4352C:p.D1451A, nonsynonymous SNV FANCD2 missense_variant nonsynonymous SNV ENSG00000144554 PASS FALSE TRUE TRUE TRUE TRUE 3.73 0.000784929 ENSG00000144554:ENST00000383807:exon44:c.A4352C:p.D1451A,ENSG00000144554:ENST00000419585:exon44:c.A4352C:p.D1451A, 1451 D/A 29,0 28,0 0,0,146 0,1,490 0,0,146 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0192 99 chr3:48491425:48491425:T:A:snp 0.733167316798394 0.0547016274864384 0.160455166401833 0.0054773082942097 0.0054773082942097 1 1 0 chr3 48491425 48491425 T A snp intronic ATRIP intronic ATRIP intron_variant intronic ENSG00000164053 PASS FALSE FALSE FALSE TRUE TRUE 2.44 0.00554675 ENSG00000164053 - - 24,0 27,0 0,2,144 0,5,480 0,2,144 0,4,431 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2823-03B-01W-0728-08,TCGA-AB-2926-03A-01W-0732-08 99,99 AOGC-02-0174,AOGC-02-0253,AOGC-02-0267,AOGC-03-0161,AOGC-08-0064 99,99,52,99,52 chr3:48493268:48493268:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 48493268 48493268 A G snp nonsynonymous SNV ATRIP:NM_001271023:exon3:c.A236G:p.Q79R,ATRIP:NM_032166:exon3:c.A515G:p.Q172R,ATRIP:NM_001271022:exon4:c.A134G:p.Q45R,ATRIP:NM_130384:exon3:c.A515G:p.Q172R, nonsynonymous SNV ATRIP missense_variant nonsynonymous SNV ENSG00000164053 PASS FALSE FALSE TRUE TRUE TRUE 3.48 0.000786164 ENSG00000164053:ENST00000454733:exon3:c.A236G:p.Q79R,ENSG00000164053:ENST00000346691:exon3:c.A515G:p.Q172R,ENSG00000164053:ENST00000357105:exon4:c.A134G:p.Q45R,ENSG00000164053:ENST00000320211:exon3:c.A515G:p.Q172R,ENSG00000164053:ENST00000421175:exon3:c.A236G:p.Q79R,ENSG00000164053:ENST00000412052:exon3:c.A236G:p.Q79R, 172 Q/R 21,0 30,0 0,0,146 0,1,489 0,0,146 0,1,479 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0026 99 chr3:48495635:48495635:G:T:snp 0.0105784635223365 -0.239482200647248 0.0936822643862294 0.0164319248826291 0.0164319248826291 1 1 0 chr3 48495635 48495635 G T snp intronic ATRIP intronic ATRIP intron_variant intronic ENSG00000164053 PASS TRUE TRUE TRUE TRUE TRUE 2.05 0.0166932 ENSG00000164053 - - 30,0 20,0 0,0,146 0,21,462 0,0,146 0,19,449 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0144,AOGC-02-0175,AOGC-02-0191,AOGC-02-0194,AOGC-02-0208,AOGC-02-0211,AOGC-02-0248,AOGC-02-0253,AOGC-02-0297,AOGC-02-0373,AOGC-02-0381,AOGC-02-0426,AOGC-02-0494,AOGC-02-0498,AOGC-02-0519,AOGC-03-0026,AOGC-03-0029,AOGC-03-0059,AOGC-08-0046,AOGC-08-0128,AOGC-14-0093 28,27,98,99,77,5,16,40,99,38,37,21,99,1,39,18,99,11,58,35,99 chr3:48505239:48505239:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 48505239 48505239 C T snp nonsynonymous SNV ATRIP:NM_001271023:exon9:c.C1562T:p.A521V,ATRIP:NM_032166:exon9:c.C1841T:p.A614V,ATRIP:NM_001271022:exon10:c.C1460T:p.A487V,ATRIP:NM_130384:exon9:c.C1841T:p.A614V, nonsynonymous SNV ATRIP missense_variant nonsynonymous SNV ENSG00000164053 PASS FALSE FALSE TRUE TRUE TRUE -2.56 0.000786164 ENSG00000164053:ENST00000346691:exon9:c.C1841T:p.A614V,ENSG00000164053:ENST00000357105:exon10:c.C1460T:p.A487V,ENSG00000164053:ENST00000320211:exon9:c.C1841T:p.A614V,ENSG00000164053:ENST00000412052:exon9:c.C1562T:p.A521V, 614 A/V 20,0 23,0 0,0,146 0,1,489 0,0,146 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0494 99 chr3:48505874:48505874:A:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 48505874 48505874 A C snp intronic ATRIP intronic ATRIP intron_variant intronic ENSG00000164053 PASS FALSE TRUE TRUE TRUE TRUE 2.3 0.000787402 ENSG00000164053 - - 13,0 7,0 0,1,145 0,0,489 0,1,140 0,0,456 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2947-03A-01W-0745-08 99 chr3:48506389:48506389:A:T:snp 0.340879557908472 -0.232704402515723 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr3 48506389 48506389 A T snp nonsynonymous SNV ATRIP:NM_001271023:exon12:c.A1936T:p.M646L,ATRIP:NM_032166:exon11:c.A2134T:p.M712L,ATRIP:NM_001271022:exon13:c.A1834T:p.M612L,ATRIP:NM_130384:exon12:c.A2215T:p.M739L, nonsynonymous SNV ATRIP missense_variant nonsynonymous SNV ENSG00000164053 PASS FALSE FALSE TRUE TRUE TRUE 1.68 0.00235479 ENSG00000164053:ENST00000346691:exon11:c.A2134T:p.M712L,ENSG00000164053:ENST00000357105:exon13:c.A1834T:p.M612L,ENSG00000164053:ENST00000320211:exon12:c.A2215T:p.M739L,ENSG00000164053:ENST00000412052:exon12:c.A1936T:p.M646L, 739 M/L 23,0 21,0 0,0,146 0,3,488 0,0,145 0,3,461 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0141,AOGC-02-0237,AOGC-05-0021 99,99,99 chr3:48506404:48506404:G:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 48506404 48506404 G T snp nonsynonymous SNV ATRIP:NM_001271023:exon12:c.G1951T:p.V651F,ATRIP:NM_032166:exon11:c.G2149T:p.V717F,ATRIP:NM_001271022:exon13:c.G1849T:p.V617F,ATRIP:NM_130384:exon12:c.G2230T:p.V744F, nonsynonymous SNV ATRIP missense_variant nonsynonymous SNV ENSG00000164053 PASS FALSE TRUE TRUE TRUE TRUE 5.51 0.000784929 ENSG00000164053:ENST00000346691:exon11:c.G2149T:p.V717F,ENSG00000164053:ENST00000357105:exon13:c.G1849T:p.V617F,ENSG00000164053:ENST00000320211:exon12:c.G2230T:p.V744F,ENSG00000164053:ENST00000412052:exon12:c.G1951T:p.V651F, 744 V/F 23,0 25,0 0,1,145 0,0,491 0,1,144 0,0,463 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2887-03A-01W-0732-08 99 chr3:142177832:142177832:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142177832 142177832 C T snp nonsynonymous SNV ATR:NM_001184:exon44:c.G7471A:p.V2491I, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS TRUE TRUE TRUE TRUE TRUE 3.77 0.000783699 ENSG00000175054:ENST00000383101:exon43:c.G7279A:p.V2427I,ENSG00000175054:ENST00000350721:exon44:c.G7471A:p.V2491I, 2427 V/I 21,0 20,0 0,0,147 0,1,490 0,0,146 0,1,479 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0046 81 chr3:142178178:142178178:A:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142178178 142178178 A C snp nonsynonymous SNV ATR:NM_001184:exon43:c.T7240G:p.S2414A, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS FALSE TRUE TRUE TRUE TRUE -5.96 0.000784929 ENSG00000175054:ENST00000383101:exon42:c.T7048G:p.S2350A,ENSG00000175054:ENST00000350721:exon43:c.T7240G:p.S2414A, 2350 S/A 35,0 20,0 0,0,146 0,1,490 0,0,146 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0004 99 chr3:142188337:142188337:A:C:snp 0.203645222317512 0.171065182829889 0.134566185463994 0.00782472613458529 0.00782472613458529 1 1 0 chr3 142188337 142188337 A C snp nonsynonymous SNV ATR:NM_001184:exon38:c.T6394G:p.Y2132D, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS FALSE FALSE FALSE TRUE TRUE 0.823 0.00788644 ENSG00000175054:ENST00000383101:exon37:c.T6202G:p.Y2068D,ENSG00000175054:ENST00000350721:exon38:c.T6394G:p.Y2132D, 2068 Y/D 23,0 21,0 0,4,142 0,6,482 0,4,142 0,6,465 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2804-03B-01W-0728-08,TCGA-AB-2811-03B-01W-0728-08,TCGA-AB-2841-03B-01W-0728-08,TCGA-AB-2928-03A-01W-0745-08 99,99,99,99 AOGC-02-0037,AOGC-02-0122,AOGC-02-0130,AOGC-02-0313,AOGC-05-0017,AOGC-08-0210 99,99,99,99,99,99 chr3:142212029:142212029:C:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142212029 142212029 C A snp nonsynonymous SNV ATR:NM_001184:exon35:c.G6023T:p.R2008L, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS FALSE TRUE TRUE TRUE TRUE 5.49 0.000784929 ENSG00000175054:ENST00000383101:exon34:c.G5831T:p.R1944L,ENSG00000175054:ENST00000350721:exon35:c.G6023T:p.R2008L, 1944 R/L 22,0 21,0 0,1,145 0,0,491 0,1,145 0,0,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2822-03D-01W-0755-09 99 chr3:142215951:142215951:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142215951 142215951 A G snp nonsynonymous SNV ATR:NM_001184:exon33:c.T5642C:p.L1881P, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS FALSE TRUE TRUE TRUE TRUE 5.39 0.000783699 ENSG00000175054:ENST00000383101:exon32:c.T5450C:p.L1817P,ENSG00000175054:ENST00000350721:exon33:c.T5642C:p.L1881P, 1817 L/P 21,0 31,0 0,0,147 0,1,490 0,0,146 0,1,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0111 99 chr3:142259997:142259997:A:G:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr3 142259997 142259997 A G snp intronic ATR intronic ATR intron_variant intronic ENSG00000175054 PASS FALSE FALSE TRUE TRUE TRUE 2.87 0.00157729 ENSG00000175054 - - 9,0 NA 0,0,145 0,2,487 0,0,140 0,1,468 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0513,AOGC-08-0253 58,99 chr3:142260005:142260005:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142260005 142260005 A G snp intronic ATR intronic ATR intron_variant intronic ENSG00000175054 PASS FALSE TRUE TRUE TRUE TRUE 2.04 0.000791139 ENSG00000175054 - - 9,0 NA 0,0,143 0,1,488 0,0,129 0,1,463 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0033 99 chr3:142261533:142261533:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142261533 142261533 T C snp nonsynonymous SNV ATR:NM_001184:exon17:c.A3424G:p.S1142G, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS FALSE FALSE TRUE TRUE TRUE 5.47 0.000784929 ENSG00000175054:ENST00000383101:exon16:c.A3232G:p.S1078G,ENSG00000175054:ENST00000350721:exon17:c.A3424G:p.S1142G, 1078 S/G 21,0 21,0 0,0,146 0,1,490 0,0,146 0,1,477 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0172 99 chr3:142268549:142268549:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142268549 142268549 A G snp intronic ATR intronic ATR intron_variant intronic ENSG00000175054 PASS FALSE TRUE TRUE TRUE TRUE 2.43 0.000786164 ENSG00000175054 - - 20,0 20,0 0,0,146 0,1,489 0,0,146 0,1,467 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0247 99 chr3:142272663:142272663:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142272663 142272663 C T snp splicing ATR(NM_001184:exon12:c.2532+4G>A) splicing ATR splice_region_variant,intron_variant splicing ENSG00000175054 PASS FALSE FALSE TRUE TRUE TRUE 0.659 0.000787402 ENSG00000175054(ENST00000350721:exon12:c.2532+4G>A,ENST00000383101:exon11:c.2340+4G>A) - - 21,0 21,0 0,0,146 0,1,488 0,0,146 0,1,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0225 99 chr3:142272708:142272708:T:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142272708 142272708 T C snp nonsynonymous SNV ATR:NM_001184:exon11:c.A2491G:p.I831V, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS TRUE TRUE TRUE TRUE TRUE 4.19 0.000783699 ENSG00000175054:ENST00000383101:exon10:c.A2299G:p.I767V,ENSG00000175054:ENST00000350721:exon11:c.A2491G:p.I831V, 767 I/V 21,0 21,0 0,1,146 0,0,491 0,1,145 0,0,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2883-03A-01W-0732-08 99 chr3:142274770:142274770:T:C:snp 0.704997875659665 -0.0655608214849913 0.173174436921412 0.00469483568075117 0.00469483568075117 1 1 0 chr3 142274770 142274770 T C snp nonsynonymous SNV ATR:NM_001184:exon10:c.A2290G:p.K764E, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS FALSE FALSE FALSE TRUE TRUE 4.16 0.00471698 ENSG00000175054:ENST00000383101:exon9:c.A2098G:p.K700E,ENSG00000175054:ENST00000350721:exon10:c.A2290G:p.K764E, 700 K/E 22,0 26,0 0,1,146 0,5,484 0,1,145 0,4,465 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2921-03A-01W-0755-09 99 AOGC-02-0056,AOGC-02-0388,AOGC-03-0036,AOGC-03-0157,AOGC-05-0013 99,99,99,91,99 chr3:142274953:142274953:C:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142274953 142274953 C A snp nonsynonymous SNV ATR:NM_001184:exon10:c.G2107T:p.V703F, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS FALSE TRUE TRUE TRUE TRUE 3.94 0.000788644 ENSG00000175054:ENST00000383101:exon9:c.G1915T:p.V639F,ENSG00000175054:ENST00000350721:exon10:c.G2107T:p.V703F, 639 V/F 22,0 26,0 0,0,146 0,1,487 0,0,146 0,1,459 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0013 99 chr3:142275399:142275399:C:T:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr3 142275399 142275399 C T snp nonsynonymous SNV ATR:NM_001184:exon9:c.G1904A:p.R635Q, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS FALSE TRUE TRUE TRUE TRUE -0.767 0.00157233 ENSG00000175054:ENST00000383101:exon8:c.G1712A:p.R571Q,ENSG00000175054:ENST00000350721:exon9:c.G1904A:p.R635Q,ENSG00000175054:ENST00000515149:exon5:c.G755A:p.R252Q, 252 R/Q 20,0 23,0 0,1,145 0,1,489 0,1,145 0,1,474 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2817-03B-01W-0728-08 99 AOGC-08-0256 99 chr3:142279108:142279108:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr3 142279108 142279108 T C snp nonsynonymous SNV ATR:NM_001184:exon6:c.A1538G:p.N513S, nonsynonymous SNV ATR missense_variant nonsynonymous SNV ENSG00000175054 PASS FALSE FALSE TRUE TRUE TRUE 1.83 0.000783699 ENSG00000175054:ENST00000350721:exon6:c.A1538G:p.N513S, 513 N/S 22,0 26,0 0,0,147 0,1,490 0,0,147 0,1,472 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0283 99 chr3:142284987:142284987:G:A:snp 0.117699294654503 0.270932069510269 0.173174436921412 0.00469483568075117 0.00469483568075117 1 1 0 chr3 142284987 142284987 G A snp nonsynonymous SNV ATR:NM_001184:exon3:c.C268T:p.H90Y, nonsynonymous SNV ATR missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000175054 PASS FALSE FALSE TRUE TRUE TRUE 3.75 0.00470219 ENSG00000175054:ENST00000507148:exon3:c.C268T:p.H90Y,ENSG00000175054:ENST00000383101:exon3:c.C268T:p.H90Y,ENSG00000175054:ENST00000350721:exon3:c.C268T:p.H90Y, 90 H/Y 22,0 24,0 0,3,144 0,3,488 0,3,144 0,3,486 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2802-03B-01W-0728-08,TCGA-AB-2813-03B-01W-0728-08,TCGA-AB-2896-03A-01W-0733-08 99,99,99 AOGC-03-0008,AOGC-03-0060,AOGC-03-0147 99,99,99 chr3:142272280:142272281:AC:-:indel:142272275 0.192350496194146 0.0725271739130443 0.0556336245195667 0.0500782472613459 0.0500782472613459 1 1 0 chr3 142272280 142272281 AC - indel:142272275 intronic ATR intronic ATR intron_variant,feature_truncation intronic ENSG00000175054 PASS TRUE TRUE TRUE TRUE TRUE 0 0.0516963 ENSG00000175054 - - 40,40 3,4 0,19,127 0,45,428 0,18,127 0,26,415 1 0 1 1 0 0 1 0 0 1 0 0 1 1 1 1 1 1 0 1 TCGA-AB-2802-03B-01W-0728-08,TCGA-AB-2827-03B-01W-0728-08,TCGA-AB-2829-03B-01W-0728-08,TCGA-AB-2839-03B-01W-0728-08,TCGA-AB-2856-03A-01W-0726-08,TCGA-AB-2869-03A-01W-0761-09,TCGA-AB-2884-03A-01W-0732-08,TCGA-AB-2892-03A-01W-0733-08,TCGA-AB-2912-03A-01W-0732-08,TCGA-AB-2918-03A-01W-0745-08,TCGA-AB-2922-03A-01W-0745-08,TCGA-AB-2923-03A-01W-0745-08,TCGA-AB-2928-03A-01W-0745-08,TCGA-AB-2929-03A-01W-0732-08,TCGA-AB-2932-03A-01W-0745-08,TCGA-AB-2934-03A-01W-0745-08,TCGA-AB-2947-03A-01W-0745-08,TCGA-AB-2952-03A-01W-0733-08,TCGA-AB-2959-03A-01W-0733-08 40,71,99,39,33,91,5,38,16,82,99,99,99,43,98,99,99,53,99 AOGC-01-0003,AOGC-02-0006,AOGC-02-0026,AOGC-02-0027,AOGC-02-0030,AOGC-02-0070,AOGC-02-0081,AOGC-02-0125,AOGC-02-0134,AOGC-02-0144,AOGC-02-0210,AOGC-02-0247,AOGC-02-0254,AOGC-02-0269,AOGC-02-0281,AOGC-02-0306,AOGC-02-0327,AOGC-02-0405,AOGC-02-0410,AOGC-02-0445,AOGC-02-0454,AOGC-02-0462,AOGC-02-0476,AOGC-02-0501,AOGC-02-0506,AOGC-02-0524,AOGC-02-0528,AOGC-02-0535,AOGC-03-0016,AOGC-03-0060,AOGC-03-0084,AOGC-03-0104,AOGC-03-0105,AOGC-03-0172,AOGC-05-0016,AOGC-08-0035,AOGC-08-0152,AOGC-08-0185,AOGC-08-0187,AOGC-08-0192,AOGC-08-0252,AOGC-08-0269,AOGC-08-0307,AOGC-08-0315,AOGC-14-0081 57,40,81,40,72,80,51,49,70,48,42,60,3,95,84,97,28,7,2,55,8,46,48,46,51,5,53,55,22,49,8,34,78,52,8,19,72,43,43,51,55,14,69,2,55 chr3:142272281:142272281:-:ACAC:indel:142272275 0.0137620143357551 0.521653543307087 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr3 142272281 142272281 - ACAC indel:142272275 intronic ATR intronic ATR intron_variant,feature_elongation intronic ENSG00000175054 PASS TRUE TRUE TRUE TRUE TRUE 0 0.00323102 ENSG00000175054 - - 40,40 3,4 0,3,143 0,1,472 0,3,143 0,1,459 1 0 1 1 0 0 1 0 0 1 0 0 1 1 1 1 1 1 0 1 TCGA-AB-2820-03B-01W-0728-08,TCGA-AB-2867-03B-01W-0728-08,TCGA-AB-2872-03A-01W-0732-08 99,35,12 AOGC-02-0325 99 chr3:142277426:142277426:-:G:indel 0.966056375478615 -0.00303327683111711 0.0712792024978744 0.0273865414710485 0.0273865414710485 1 1 0 chr3 142277426 142277426 - G indel intronic ATR intronic ATR intron_variant,feature_elongation intronic ENSG00000175054 PASS TRUE TRUE TRUE TRUE TRUE 3.09 0.0298126 ENSG00000175054 - - 23,0 34,0 0,8,123 1,25,430 0,8,122 1,21,401 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 0.264543115900909 1 0 1 TCGA-AB-2803-03B-01W-0728-08,TCGA-AB-2806-03B-01W-0728-08,TCGA-AB-2821-03B-01W-0728-08,TCGA-AB-2827-03B-01W-0728-08,TCGA-AB-2835-03B-01W-0728-08,TCGA-AB-2894-03A-01W-0733-08,TCGA-AB-2908-03A-01W-0745-08,TCGA-AB-2945-03A-01W-0733-08 99,99,99,99,51,99,99,99 AOGC-02-0004,AOGC-02-0015,AOGC-02-0026,AOGC-02-0047,AOGC-02-0081,AOGC-02-0140,AOGC-02-0164,AOGC-02-0171,AOGC-02-0264,AOGC-02-0292,AOGC-02-0297,AOGC-02-0361,AOGC-02-0443,AOGC-02-0448,AOGC-02-0467,AOGC-02-0471,AOGC-02-0513,AOGC-03-0047,AOGC-03-0152,AOGC-05-0019,AOGC-05-0021,AOGC-08-0163,AOGC-08-0178,AOGC-08-0212,AOGC-08-0253,AOGC-08-0318 99,79,99,99,99,99,99,24,99,99,99,99,99,99,99,53,78,27,85,99,99,66,99,62,30,99 chr5:68680643:68680643:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 68680643 68680643 T C snp synonymous SNV RAD17:NM_133340:exon5:c.T33C:p.F11F,RAD17:NM_133343:exon7:c.T528C:p.F176F,RAD17:NM_001278622:exon7:c.T528C:p.F176F,RAD17:NM_002873:exon6:c.T528C:p.F176F,RAD17:NM_133339:exon5:c.T561C:p.F187F,RAD17:NM_133342:exon7:c.T528C:p.F176F,RAD17:NM_133341:exon5:c.T270C:p.F90F,RAD17:NM_133338:exon8:c.T528C:p.F176F,RAD17:NM_133344:exon6:c.T528C:p.F176F, synonymous SNV RAD17 non_coding_exon_variant,nc_transcript_variant synonymous SNV ENSG00000152942 PASS FALSE TRUE TRUE TRUE TRUE 2.61 0.000787402 ENSG00000152942:ENST00000354868:exon8:c.T528C:p.F176F,ENSG00000152942:ENST00000282891:exon5:c.T270C:p.F90F,ENSG00000152942:ENST00000361732:exon7:c.T528C:p.F176F,ENSG00000152942:ENST00000521422:exon6:c.T33C:p.F11F,ENSG00000152942:ENST00000358030:exon5:c.T33C:p.F11F,ENSG00000152942:ENST00000380774:exon5:c.T561C:p.F187F,ENSG00000152942:ENST00000345306:exon6:c.T528C:p.F176F,ENSG00000152942:ENST00000512785:exon6:c.T33C:p.F11F,ENSG00000152942:ENST00000354312:exon7:c.T528C:p.F176F,ENSG00000152942:ENST00000509734:exon7:c.T561C:p.F187F,ENSG00000152942:ENST00000305138:exon6:c.T528C:p.F176F, - - 22,0 20,0 0,0,145 0,1,489 0,0,145 0,1,479 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0073 99 chr5:68682299:68682299:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 68682299 68682299 C T snp intronic RAD17 intronic RAD17 splice_region_variant,intron_variant intronic ENSG00000152942 PASS FALSE FALSE TRUE TRUE TRUE -2.7 0.000794913 ENSG00000152942 - - 10,0 9,0 0,0,145 0,1,483 0,0,145 0,1,436 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0431 99 chr5:68684853:68684853:T:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 68684853 68684853 T G snp intronic RAD17 intronic RAD17 splice_region_variant,intron_variant intronic ENSG00000152942 PASS TRUE TRUE TRUE TRUE TRUE -1.38 0.000789889 ENSG00000152942 - - 8,0 2,0 0,1,141 0,0,491 0,1,118 0,0,466 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2828-03C-01W-0761-09 99 chr5:68687690:68687690:A:G:snp 0.675730396862748 0.102201257861636 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr5 68687690 68687690 A G snp nonsynonymous SNV RAD17:NM_133340:exon10:c.A544G:p.M182V,RAD17:NM_133343:exon12:c.A1039G:p.M347V,RAD17:NM_001278622:exon12:c.A1039G:p.M347V,RAD17:NM_002873:exon11:c.A1039G:p.M347V,RAD17:NM_133339:exon10:c.A1072G:p.M358V,RAD17:NM_133342:exon12:c.A1039G:p.M347V,RAD17:NM_133341:exon10:c.A781G:p.M261V,RAD17:NM_133338:exon13:c.A1039G:p.M347V,RAD17:NM_133344:exon11:c.A1039G:p.M347V, nonsynonymous SNV RAD17 missense_variant nonsynonymous SNV ENSG00000152942 PASS FALSE FALSE TRUE TRUE TRUE -4.67 0.00236593 ENSG00000152942:ENST00000508320:exon4:c.A298G:p.M100V,ENSG00000152942:ENST00000354868:exon13:c.A1039G:p.M347V,ENSG00000152942:ENST00000282891:exon10:c.A781G:p.M261V,ENSG00000152942:ENST00000361732:exon12:c.A1039G:p.M347V,ENSG00000152942:ENST00000521422:exon11:c.A544G:p.M182V,ENSG00000152942:ENST00000358030:exon10:c.A544G:p.M182V,ENSG00000152942:ENST00000380774:exon10:c.A1072G:p.M358V,ENSG00000152942:ENST00000345306:exon11:c.A1039G:p.M347V,ENSG00000152942:ENST00000354312:exon12:c.A1039G:p.M347V,ENSG00000152942:ENST00000509734:exon12:c.A1072G:p.M358V,ENSG00000152942:ENST00000305138:exon11:c.A1039G:p.M347V, 182 M/V 21,0 22,0 0,1,144 0,2,487 0,1,144 0,2,427 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2881-03A-01W-0732-08 99 AOGC-02-0369,AOGC-14-0141 99,99 chr5:68689162:68689162:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 68689162 68689162 T C snp intronic RAD17 intronic RAD17 intron_variant intronic ENSG00000152942 PASS FALSE TRUE TRUE TRUE TRUE 2.25 0.000787402 ENSG00000152942 - - 21,0 9,0 0,0,145 0,1,489 0,0,144 0,1,481 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0224 99 chr5:68692217:68692217:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 68692217 68692217 T C snp intronic RAD17 intronic RAD17 splice_region_variant,intron_variant intronic ENSG00000152942 PASS FALSE FALSE TRUE TRUE TRUE 1.11 0.000787402 ENSG00000152942 - - 28,0 22,0 0,0,145 0,1,489 0,0,145 0,1,456 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0100 99 chr5:68709884:68709884:G:A:snp 0.370601625965528 0.169716088328076 0.189553423814011 0.00391236306729264 0.00391236306729264 1 1 0 chr5 68709884 68709884 G A snp nonsynonymous SNV RAD17:NM_133340:exon16:c.G1283A:p.R428K,RAD17:NM_133343:exon18:c.G1778A:p.R593K,RAD17:NM_001278622:exon18:c.G1778A:p.R593K,RAD17:NM_002873:exon17:c.G1778A:p.R593K,RAD17:NM_133339:exon16:c.G1811A:p.R604K,RAD17:NM_133342:exon18:c.G1778A:p.R593K,RAD17:NM_133341:exon16:c.G1520A:p.R507K,RAD17:NM_133338:exon19:c.G1778A:p.R593K,RAD17:NM_133344:exon17:c.G1778A:p.R593K, nonsynonymous SNV RAD17 missense_variant nonsynonymous SNV ENSG00000152942 PASS FALSE FALSE FALSE TRUE TRUE 2.09 0.00392465 ENSG00000152942:ENST00000354868:exon19:c.G1778A:p.R593K,ENSG00000152942:ENST00000282891:exon16:c.G1520A:p.R507K,ENSG00000152942:ENST00000361732:exon18:c.G1778A:p.R593K,ENSG00000152942:ENST00000521422:exon17:c.G1283A:p.R428K,ENSG00000152942:ENST00000358030:exon16:c.G1283A:p.R428K,ENSG00000152942:ENST00000380774:exon16:c.G1811A:p.R604K,ENSG00000152942:ENST00000345306:exon17:c.G1778A:p.R593K,ENSG00000152942:ENST00000354312:exon18:c.G1778A:p.R593K,ENSG00000152942:ENST00000509734:exon18:c.G1811A:p.R604K,ENSG00000152942:ENST00000305138:exon17:c.G1778A:p.R593K, 428 R/K 23,0 30,0 0,2,144 0,3,488 0,2,143 0,3,472 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2807-03B-01W-0728-08,TCGA-AB-2903-03A-01W-0761-09 99,99 AOGC-03-0129,AOGC-08-0004,AOGC-08-0139 99,99,99 chr5:68709886:68709886:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 68709886 68709886 G C snp nonsynonymous SNV RAD17:NM_133340:exon16:c.G1285C:p.E429Q,RAD17:NM_133343:exon18:c.G1780C:p.E594Q,RAD17:NM_001278622:exon18:c.G1780C:p.E594Q,RAD17:NM_002873:exon17:c.G1780C:p.E594Q,RAD17:NM_133339:exon16:c.G1813C:p.E605Q,RAD17:NM_133342:exon18:c.G1780C:p.E594Q,RAD17:NM_133341:exon16:c.G1522C:p.E508Q,RAD17:NM_133338:exon19:c.G1780C:p.E594Q,RAD17:NM_133344:exon17:c.G1780C:p.E594Q, nonsynonymous SNV RAD17 missense_variant nonsynonymous SNV ENSG00000152942 PASS FALSE TRUE TRUE TRUE TRUE 5.35 0.000784929 ENSG00000152942:ENST00000354868:exon19:c.G1780C:p.E594Q,ENSG00000152942:ENST00000282891:exon16:c.G1522C:p.E508Q,ENSG00000152942:ENST00000361732:exon18:c.G1780C:p.E594Q,ENSG00000152942:ENST00000521422:exon17:c.G1285C:p.E429Q,ENSG00000152942:ENST00000358030:exon16:c.G1285C:p.E429Q,ENSG00000152942:ENST00000380774:exon16:c.G1813C:p.E605Q,ENSG00000152942:ENST00000345306:exon17:c.G1780C:p.E594Q,ENSG00000152942:ENST00000354312:exon18:c.G1780C:p.E594Q,ENSG00000152942:ENST00000509734:exon18:c.G1813C:p.E605Q,ENSG00000152942:ENST00000305138:exon17:c.G1780C:p.E594Q, 429 E/Q 23,0 30,0 0,0,146 0,1,490 0,0,145 0,1,474 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0437 99 chr5:131911535:131911535:A:C:snp 0.27105525402704 -0.233070866141732 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr5 131911535 131911535 A C snp nonsynonymous SNV RAD50:NM_005732:exon3:c.A280C:p.I94L, nonsynonymous SNV RAD50 missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000113522 PASS FALSE FALSE FALSE TRUE TRUE -10.2 0.00313972 ENSG00000113522:ENST00000533482:exon3:c.A280C:p.I94L,ENSG00000113522:ENST00000265335:exon3:c.A280C:p.I94L,ENSG00000113522:ENST00000423956:exon3:c.A280C:p.I94L,ENSG00000113522:ENST00000453394:exon3:c.A280C:p.I94L, 94 I/L 21,0 20,0 0,0,146 0,4,487 0,0,145 0,4,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0254,AOGC-02-0494,AOGC-02-0496,AOGC-05-0021 99,99,99,99 chr5:131915005:131915005:G:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131915005 131915005 G A snp splicing RAD50(NM_005732:exon4:c.366-4G>A) splicing RAD50 splice_region_variant,intron_variant,NMD_transcript_variant splicing ENSG00000113522 PASS TRUE TRUE TRUE TRUE TRUE -11 0.000789889 ENSG00000113522(ENST00000416135:exon4:c.69-4G>A,ENST00000265335:exon4:c.366-4G>A,ENST00000533482:exon4:c.301-4G>A,ENST00000423956:exon4:c.366-4G>A,ENST00000453394:exon4:c.366-4G>A) - - 21,0 20,0 0,1,143 0,0,489 0,1,143 0,0,474 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2877-03A-01W-0732-08 99 chr5:131915673:131915673:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131915673 131915673 G A snp nonsynonymous SNV RAD50:NM_005732:exon5:c.G671A:p.R224H, nonsynonymous SNV RAD50 missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000113522 PASS FALSE TRUE TRUE TRUE TRUE 4.05 0.000787402 ENSG00000113522:ENST00000265335:exon5:c.G671A:p.R224H,ENSG00000113522:ENST00000423956:exon5:c.G671A:p.R224H,ENSG00000113522:ENST00000453394:exon5:c.G671A:p.R224H,ENSG00000113522:ENST00000378823:exon5:c.G254A:p.R85H, 224 R/H 27,0 22,0 0,0,145 0,1,489 0,0,145 0,1,476 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0091 99 chr5:131923545:131923545:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131923545 131923545 A T snp intronic RAD50 intronic RAD50 intron_variant,NMD_transcript_variant intronic ENSG00000113522 PASS FALSE TRUE TRUE TRUE TRUE 3.55 0.000794913 ENSG00000113522 - - 7,0 4,0 0,0,145 0,1,483 0,0,131 0,1,450 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0459 99 chr5:131923673:131923673:G:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr5 131923673 131923673 G T snp nonsynonymous SNV RAD50:NM_005732:exon7:c.G943T:p.V315L, nonsynonymous SNV RAD50 missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000113522 PASS FALSE FALSE TRUE TRUE TRUE 5.42 0.0015748 ENSG00000113522:ENST00000265335:exon7:c.G943T:p.V315L,ENSG00000113522:ENST00000423956:exon7:c.G943T:p.V315L,ENSG00000113522:ENST00000453394:exon7:c.G943T:p.V315L,ENSG00000113522:ENST00000378823:exon7:c.G526T:p.V176L, 315 V/L 24,0 20,0 0,0,146 0,2,487 0,0,145 0,2,476 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0052,AOGC-14-0041 99,99 chr5:131923710:131923710:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131923710 131923710 G A snp nonsynonymous SNV RAD50:NM_005732:exon7:c.G980A:p.R327H, nonsynonymous SNV RAD50 missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000113522 PASS FALSE FALSE TRUE TRUE TRUE 5.42 0.000787402 ENSG00000113522:ENST00000265335:exon7:c.G980A:p.R327H,ENSG00000113522:ENST00000423956:exon7:c.G980A:p.R327H,ENSG00000113522:ENST00000453394:exon7:c.G980A:p.R327H,ENSG00000113522:ENST00000378823:exon7:c.G563A:p.R188H, 327 R/H 24,0 20,0 0,0,146 0,1,488 0,0,145 0,1,478 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0088 99 chr5:131925491:131925491:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131925491 131925491 G C snp nonsynonymous SNV RAD50:NM_005732:exon9:c.G1414C:p.D472H, nonsynonymous SNV RAD50 missense_variant,NMD_transcript_variant nonsynonymous SNV ENSG00000113522 PASS FALSE TRUE TRUE TRUE TRUE 5.29 0.000792393 ENSG00000113522:ENST00000265335:exon9:c.G1414C:p.D472H,ENSG00000113522:ENST00000423956:exon9:c.G1414C:p.D472H,ENSG00000113522:ENST00000453394:exon9:c.G1414C:p.D472H,ENSG00000113522:ENST00000378823:exon9:c.G997C:p.D333H, 472 D/H 31,0 22,0 0,0,145 0,1,485 0,0,145 0,1,392 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0019 99 chr5:131927692:131927692:A:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131927692 131927692 A C snp nonsynonymous SNV RAD50:NM_005732:exon11:c.A1759C:p.I587L, nonsynonymous SNV RAD50 missense_variant nonsynonymous SNV ENSG00000113522 PASS FALSE TRUE TRUE TRUE TRUE 6.06 0.000788644 ENSG00000113522:ENST00000265335:exon11:c.A1759C:p.I587L,ENSG00000113522:ENST00000453394:exon10:c.A1576C:p.I526L,ENSG00000113522:ENST00000378823:exon11:c.A1342C:p.I448L, 448 I/L 23,0 20,0 0,0,145 0,1,488 0,0,145 0,1,453 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0333 99 chr5:131939625:131939625:A:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131939625 131939625 A G snp nonsynonymous SNV RAD50:NM_005732:exon15:c.A2411G:p.D804G, nonsynonymous SNV RAD50 missense_variant nonsynonymous SNV ENSG00000113522 PASS TRUE TRUE TRUE TRUE TRUE 5.67 0.000784929 ENSG00000113522:ENST00000265335:exon15:c.A2411G:p.D804G,ENSG00000113522:ENST00000378823:exon15:c.A1994G:p.D665G, 665 D/G 23,0 21,0 0,1,145 0,0,491 0,1,144 0,0,477 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2932-03A-01W-0745-08 99 chr5:131940485:131940485:T:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131940485 131940485 T A snp intronic RAD50 intronic RAD50 intron_variant,NMD_transcript_variant intronic ENSG00000113522 PASS FALSE TRUE TRUE TRUE TRUE 3.62 0.000787402 ENSG00000113522 - - 7,0 25,0 0,0,145 0,1,489 0,0,145 0,1,464 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0457 99 chr5:131973890:131973890:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131973890 131973890 G A snp nonsynonymous SNV RAD50:NM_005732:exon23:c.G3593A:p.R1198Q, nonsynonymous SNV RAD50 missense_variant nonsynonymous SNV ENSG00000113522 PASS FALSE TRUE TRUE TRUE TRUE 5.95 0.000786164 ENSG00000113522:ENST00000265335:exon23:c.G3593A:p.R1198Q,ENSG00000113522:ENST00000378823:exon23:c.G3176A:p.R1059Q, 1059 R/Q 21,0 22,0 0,0,145 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-05-0012 99 chr5:131976416:131976416:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131976416 131976416 A G snp nonsynonymous SNV RAD50:NM_005732:exon24:c.A3671G:p.N1224S, nonsynonymous SNV RAD50 missense_variant nonsynonymous SNV ENSG00000113522 PASS FALSE TRUE TRUE TRUE TRUE 6.16 0.000786164 ENSG00000113522:ENST00000265335:exon24:c.A3671G:p.N1224S,ENSG00000113522:ENST00000378823:exon24:c.A3254G:p.N1085S, 1085 N/S 26,0 23,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0059 99 chr5:131977906:131977906:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 131977906 131977906 G C snp nonsynonymous SNV RAD50:NM_005732:exon25:c.G3789C:p.Q1263H, nonsynonymous SNV RAD50 missense_variant nonsynonymous SNV ENSG00000113522 PASS FALSE FALSE TRUE TRUE TRUE 4.75 0.000787402 ENSG00000113522:ENST00000265335:exon25:c.G3789C:p.Q1263H,ENSG00000113522:ENST00000378823:exon25:c.G3372C:p.Q1124H, 1124 Q/H 20,0 21,0 0,0,145 0,1,489 0,0,145 0,1,475 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0158 91 chr5:131977978:131977978:C:T:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr5 131977978 131977978 C T snp synonymous SNV RAD50:NM_005732:exon25:c.C3861T:p.Y1287Y, synonymous SNV RAD50 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000113522 PASS FALSE FALSE TRUE TRUE TRUE 4.94 0.00156986 ENSG00000113522:ENST00000265335:exon25:c.C3861T:p.Y1287Y,ENSG00000113522:ENST00000378823:exon25:c.C3444T:p.Y1148Y, - - 20,0 21,0 0,0,146 0,2,489 0,0,145 0,2,486 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0105,AOGC-05-0001 99,99 chr5:68682304:68682307:ATTA:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr5 68682304 68682307 ATTA - indel intronic RAD17 intronic RAD17 intron_variant,feature_truncation intronic ENSG00000152942 PASS TRUE TRUE TRUE TRUE TRUE 3.25 0.000794913 ENSG00000152942 - - 10,0 9,0 0,0,145 0,1,483 0,0,145 0,1,435 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0465 99 chr6:35423528:35423528:C:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr6 35423528 35423528 C T snp nonsynonymous SNV FANCE:NM_021922:exon2:c.C253T:p.P85S, nonsynonymous SNV FANCE missense_variant nonsynonymous SNV ENSG00000112039 PASS FALSE FALSE TRUE TRUE TRUE 5.37 0.000810373 ENSG00000112039:ENST00000229769:exon2:c.C253T:p.P85S, 85 P/S 28,0 30,0 0,1,144 0,0,472 0,1,144 0,0,428 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2933-03A-01W-0732-08 99 chr6:35426122:35426122:G:C:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr6 35426122 35426122 G C snp nonsynonymous SNV FANCE:NM_021922:exon5:c.G1018C:p.G340R, nonsynonymous SNV FANCE missense_variant nonsynonymous SNV ENSG00000112039 PASS FALSE TRUE TRUE TRUE TRUE 3.6 0.00157233 ENSG00000112039:ENST00000229769:exon5:c.G1018C:p.G340R, 340 G/R 24,0 21,0 0,1,144 0,1,490 0,1,144 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2942-03A-01W-0733-08 99 AOGC-02-0079 99 chr6:35426196:35426196:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr6 35426196 35426196 C T snp synonymous SNV FANCE:NM_021922:exon5:c.C1092T:p.T364T, synonymous SNV FANCE synonymous_variant synonymous SNV ENSG00000112039 PASS FALSE TRUE TRUE TRUE TRUE 4.45 0.000786164 ENSG00000112039:ENST00000229769:exon5:c.C1092T:p.T364T, 364 T 24,0 21,0 0,0,145 0,1,490 0,0,145 0,1,490 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-14-0437 99 chr6:35427104:35427104:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr6 35427104 35427104 G A snp splicing FANCE(NM_021922:exon6:c.1114-4G>A) splicing FANCE splice_region_variant,intron_variant splicing ENSG00000112039 PASS FALSE TRUE TRUE TRUE TRUE -1.13 0.000786164 ENSG00000112039(ENST00000229769:exon6:c.1114-4G>A) - - 20,0 22,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0454 99 chr6:35427110:35427110:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr6 35427110 35427110 C T snp synonymous SNV FANCE:NM_021922:exon6:c.C1116T:p.I372I, synonymous SNV FANCE splice_region_variant,synonymous_variant synonymous SNV ENSG00000112039 PASS FALSE TRUE TRUE TRUE TRUE 2.75 0.000786164 ENSG00000112039:ENST00000229769:exon6:c.C1116T:p.I372I, 372 I 20,0 22,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0162 99 chr6:35428343:35428343:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr6 35428343 35428343 T C snp nonsynonymous SNV FANCE:NM_021922:exon8:c.T1331C:p.L444P, nonsynonymous SNV FANCE missense_variant nonsynonymous SNV ENSG00000112039 PASS FALSE TRUE TRUE TRUE TRUE 4.97 0.000786164 ENSG00000112039:ENST00000229769:exon8:c.T1331C:p.L444P, 444 L/P 21,0 20,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0467 99 chr6:35428345:35428345:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr6 35428345 35428345 C T snp nonsynonymous SNV FANCE:NM_021922:exon8:c.C1333T:p.P445S, nonsynonymous SNV FANCE missense_variant nonsynonymous SNV ENSG00000112039 PASS FALSE TRUE TRUE TRUE TRUE 1.65 0.000786164 ENSG00000112039:ENST00000229769:exon8:c.C1333T:p.P445S, 445 P/S 21,0 20,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0198 99 chr6:35434010:35434010:C:T:snp 0.27105525402704 -0.233070866141732 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr6 35434010 35434010 C T snp intronic FANCE intronic FANCE intron_variant intronic ENSG00000112039 PASS FALSE FALSE TRUE TRUE TRUE 3.94 0.00314961 ENSG00000112039 - - 20,0 27,0 0,0,146 0,4,485 0,0,144 0,4,424 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0065,AOGC-03-0104,AOGC-08-0291,AOGC-14-0064 99,99,38,43 chr6:35434119:35434119:C:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr6 35434119 35434119 C G snp synonymous SNV FANCE:NM_021922:exon10:c.C1608G:p.P536P, synonymous SNV FANCE synonymous_variant synonymous SNV ENSG00000112039 PASS FALSE TRUE TRUE TRUE TRUE 2.9 0.000786164 ENSG00000112039:ENST00000229769:exon10:c.C1608G:p.P536P, 536 P 20,0 27,0 0,1,144 0,0,491 0,1,143 0,0,491 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2836-03B-01W-0728-08 99 chr6:35425714:35425714:-:C:indel 1.95687828118887e-10 0.783094098883573 0.123037322324538 0.00938967136150235 0.00938967136150235 1 1 0 chr6 35425714 35425714 - C indel frameshift insertion FANCE:NM_021922:exon4:c.922_923insC:p.A308fs, frameshift insertion FANCE frameshift_variant,feature_elongation frameshift insertion ENSG00000112039 PASS TRUE TRUE TRUE TRUE TRUE 2.27 0.00941915 ENSG00000112039:ENST00000229769:exon4:c.922_923insC:p.A308fs, 308 - 190,22 29,0 0,12,134 0,0,491 0,12,133 0,0,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2802-03B-01W-0728-08,TCGA-AB-2806-03B-01W-0728-08,TCGA-AB-2826-03B-01W-0728-08,TCGA-AB-2854-03B-01W-0728-08,TCGA-AB-2857-03B-01W-0728-08,TCGA-AB-2863-03B-01W-0728-08,TCGA-AB-2878-03A-01W-0732-08,TCGA-AB-2893-03A-01W-0733-08,TCGA-AB-2896-03A-01W-0733-08,TCGA-AB-2935-03A-01W-0745-08,TCGA-AB-2946-03A-01W-0755-09,TCGA-AB-2950-03A-01W-0733-08 7,2,99,41,33,63,24,41,99,46,31,62 chr6:35427116:35427118:CTT:-:indel 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr6 35427116 35427118 CTT - indel nonframeshift deletion FANCE:NM_021922:exon6:c.1122_1124del:p.374_375del, nonframeshift deletion FANCE missense_variant,feature_truncation nonframeshift deletion ENSG00000112039 PASS TRUE TRUE TRUE TRUE TRUE 4.88 0.000786164 ENSG00000112039:ENST00000229769:exon6:c.1122_1124del:p.374_375del, 374-375 SL/S 20,0 22,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0026 99 chr7:7678772:7678772:G:T:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr7 7678772 7678772 G T snp nonsynonymous SNV RPA3:NM_002947:exon6:c.C103A:p.H35N, nonsynonymous SNV RPA3 missense_variant nonsynonymous SNV ENSG00000106399 PASS TRUE TRUE TRUE TRUE TRUE 4.62 0.000786164 ENSG00000106399:ENST00000396682:exon3:c.C103A:p.H35N,ENSG00000106399:ENST00000223129:exon6:c.C103A:p.H35N, 35 H/N 20,0 10,0 0,1,144 0,0,491 0,1,144 0,0,481 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2959-03A-01W-0733-08 99 chr7:7679959:7679959:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr7 7679959 7679959 G C snp nonsynonymous SNV RPA3:NM_002947:exon5:c.C91G:p.L31V, nonsynonymous SNV RPA3 missense_variant nonsynonymous SNV ENSG00000106399 PASS FALSE FALSE TRUE TRUE TRUE 4.2 0.000786164 ENSG00000106399:ENST00000396682:exon2:c.C91G:p.L31V,ENSG00000106399:ENST00000223129:exon5:c.C91G:p.L31V, 31 L/V 44,0 31,0 0,0,145 0,1,490 0,0,145 0,1,482 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0025 99 chr7:7680024:7680024:C:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr7 7680024 7680024 C G snp nonsynonymous SNV RPA3:NM_002947:exon5:c.G26C:p.R9T, nonsynonymous SNV RPA3 missense_variant nonsynonymous SNV ENSG00000106399 PASS TRUE TRUE TRUE TRUE TRUE -3.56 0.000786164 ENSG00000106399:ENST00000396682:exon2:c.G26C:p.R9T,ENSG00000106399:ENST00000223129:exon5:c.G26C:p.R9T, 9 R/T 44,0 31,0 0,1,144 0,0,491 0,1,144 0,0,491 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2864-03B-01W-0728-08 99 chr7:152345762:152345762:A:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr7 152345762 152345762 A C snp nonsynonymous SNV XRCC2:NM_005431:exon3:c.T808G:p.F270V, nonsynonymous SNV XRCC2 missense_variant nonsynonymous SNV ENSG00000196584 PASS FALSE FALSE FALSE TRUE TRUE 5.49 0.000786164 ENSG00000196584:ENST00000359321:exon3:c.T808G:p.F270V, 270 F/V 8,0 9,0 0,1,144 0,0,491 0,1,141 0,0,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2829-03B-01W-0728-08 62 chr7:152346341:152346341:C:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr7 152346341 152346341 C G snp nonsynonymous SNV XRCC2:NM_005431:exon3:c.G229C:p.E77Q, nonsynonymous SNV XRCC2 missense_variant nonsynonymous SNV ENSG00000196584 PASS FALSE TRUE TRUE TRUE TRUE 5.39 0.000796178 ENSG00000196584:ENST00000359321:exon3:c.G229C:p.E77Q, 77 E/Q 21,0 29,0 0,1,144 0,0,483 0,1,144 0,0,408 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2820-03B-01W-0728-08 99 chr7:152357883:152357883:A:G:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr7 152357883 152357883 A G snp intronic XRCC2 intronic XRCC2 intron_variant intronic ENSG00000196584 PASS FALSE FALSE TRUE TRUE TRUE 4.23 0.00159236 ENSG00000196584 - - 13,0 11,0 0,1,141 0,1,485 0,1,135 0,0,430 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2894-03A-01W-0733-08 44 AOGC-02-0022 27 chr8:90955526:90955526:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr8 90955526 90955526 A G snp synonymous SNV NBN:NM_002485:exon14:c.T2139C:p.A713A, synonymous SNV NBN 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000104320 PASS FALSE TRUE TRUE TRUE TRUE 3.45 0.000784929 ENSG00000104320:ENST00000409330:exon14:c.T1893C:p.A631A,ENSG00000104320:ENST00000265433:exon14:c.T2139C:p.A713A, - - 22,0 26,0 0,0,146 0,1,490 0,0,145 0,1,485 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0159 99 chr8:90965588:90965588:C:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr8 90965588 90965588 C A snp nonsynonymous SNV NBN:NM_002485:exon11:c.G1729T:p.D577Y, nonsynonymous SNV NBN missense_variant nonsynonymous SNV ENSG00000104320 PASS FALSE TRUE TRUE TRUE TRUE 1.32 0.000784929 ENSG00000104320:ENST00000409330:exon11:c.G1483T:p.D495Y,ENSG00000104320:ENST00000265433:exon11:c.G1729T:p.D577Y, 577 D/Y 26,0 21,0 0,0,146 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0182 99 chr8:90965597:90965597:A:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr8 90965597 90965597 A T snp nonsynonymous SNV NBN:NM_002485:exon11:c.T1720A:p.L574I, nonsynonymous SNV NBN missense_variant nonsynonymous SNV ENSG00000104320 PASS FALSE FALSE TRUE TRUE TRUE 1 0.000784929 ENSG00000104320:ENST00000409330:exon11:c.T1474A:p.L492I,ENSG00000104320:ENST00000265433:exon11:c.T1720A:p.L574I, 574 L/I 26,0 21,0 0,0,146 0,1,490 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0044 99 chr8:90983460:90983460:G:A:snp 0.370601625965528 0.169716088328076 0.189553423814011 0.00391236306729264 0.00391236306729264 1 1 0 chr8 90983460 90983460 G A snp nonsynonymous SNV NBN:NM_002485:exon6:c.C643T:p.R215W, nonsynonymous SNV NBN missense_variant nonsynonymous SNV ENSG00000104320 PASS FALSE FALSE FALSE TRUE TRUE 4.96 0.00393701 ENSG00000104320:ENST00000409330:exon6:c.C397T:p.R133W,ENSG00000104320:ENST00000519426:exon4:c.C379T:p.R127W,ENSG00000104320:ENST00000517772:exon4:c.C397T:p.R133W,ENSG00000104320:ENST00000265433:exon6:c.C643T:p.R215W, 133 R/W 21,0 14,0 0,2,143 0,3,487 0,2,143 0,2,477 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2848-03B-01W-0728-08,TCGA-AB-2855-03B-01W-0728-08 99,99 AOGC-02-0164,AOGC-02-0249,AOGC-02-0250 98,51,99 chr8:90983475:90983475:C:A:snp 0.0736113257430485 0.437106918238994 0.244327346963028 0.00234741784037559 0.00234741784037559 1 1 0 chr8 90983475 90983475 C A snp nonsynonymous SNV NBN:NM_002485:exon6:c.G628T:p.V210F, nonsynonymous SNV NBN missense_variant nonsynonymous SNV ENSG00000104320 PASS FALSE FALSE TRUE TRUE TRUE -1.85 0.0023622 ENSG00000104320:ENST00000409330:exon6:c.G382T:p.V128F,ENSG00000104320:ENST00000519426:exon4:c.G364T:p.V122F,ENSG00000104320:ENST00000517772:exon4:c.G382T:p.V128F,ENSG00000104320:ENST00000265433:exon6:c.G628T:p.V210F, 128 V/F 21,0 21,0 0,2,143 0,1,489 0,2,143 0,1,478 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2877-03A-01W-0732-08,TCGA-AB-2933-03A-01W-0732-08 99,99 AOGC-01-0003 99 chr8:90990521:90990521:T:C:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr8 90990521 90990521 T C snp nonsynonymous SNV NBN:NM_002485:exon5:c.A511G:p.I171V, nonsynonymous SNV NBN missense_variant nonsynonymous SNV ENSG00000104320 PASS FALSE FALSE TRUE TRUE TRUE 4.81 0.00157978 ENSG00000104320:ENST00000517337:exon6:c.A265G:p.I89V,ENSG00000104320:ENST00000409330:exon5:c.A265G:p.I89V,ENSG00000104320:ENST00000517772:exon3:c.A265G:p.I89V,ENSG00000104320:ENST00000265433:exon5:c.A511G:p.I171V, 89 I/V 35,0 26,0 0,0,145 0,2,486 0,0,145 0,2,447 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0522,AOGC-08-0170 97,90 chr8:90992986:90992986:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr8 90992986 90992986 C T snp nonsynonymous SNV NBN:NM_002485:exon4:c.G456A:p.M152I, nonsynonymous SNV NBN missense_variant nonsynonymous SNV ENSG00000104320 PASS FALSE TRUE TRUE TRUE TRUE 5.75 0.000786164 ENSG00000104320:ENST00000517337:exon5:c.G210A:p.M70I,ENSG00000104320:ENST00000409330:exon4:c.G210A:p.M70I,ENSG00000104320:ENST00000517772:exon2:c.G210A:p.M70I,ENSG00000104320:ENST00000265433:exon4:c.G456A:p.M152I, 70 M/I 22,0 21,0 0,0,146 0,1,489 0,0,145 0,1,469 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0280 99 chr8:90993061:90993061:A:G:snp 0.176975649052251 -0.233807266982622 0.173174436921412 0.00469483568075117 0.00469483568075117 1 1 0 chr8 90993061 90993061 A G snp synonymous SNV NBN:NM_002485:exon4:c.T381C:p.A127A, synonymous SNV NBN 3_prime_UTR_variant,NMD_transcript_variant synonymous SNV ENSG00000104320 PASS FALSE FALSE FALSE TRUE TRUE 5.75 0.00471698 ENSG00000104320:ENST00000517337:exon5:c.T135C:p.A45A,ENSG00000104320:ENST00000409330:exon4:c.T135C:p.A45A,ENSG00000104320:ENST00000517772:exon2:c.T135C:p.A45A,ENSG00000104320:ENST00000265433:exon4:c.T381C:p.A127A, - - 22,0 21,0 0,0,146 0,6,484 0,0,146 0,6,473 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0037,AOGC-02-0106,AOGC-02-0149,AOGC-02-0312,AOGC-03-0024,AOGC-08-0032 99,99,99,99,99,99 chr8:90993645:90993645:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr8 90993645 90993645 G A snp nonsynonymous SNV NBN:NM_002485:exon3:c.C278T:p.S93L, nonsynonymous SNV NBN missense_variant nonsynonymous SNV ENSG00000104320 PASS FALSE TRUE TRUE TRUE TRUE 5.71 0.000786164 ENSG00000104320:ENST00000517337:exon4:c.C32T:p.S11L,ENSG00000104320:ENST00000409330:exon3:c.C32T:p.S11L,ENSG00000104320:ENST00000519426:exon3:c.C278T:p.S93L,ENSG00000104320:ENST00000517772:exon1:c.C32T:p.S11L,ENSG00000104320:ENST00000265433:exon3:c.C278T:p.S93L, 11 S/L 28,0 29,0 0,0,145 0,1,490 0,0,145 0,1,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0264 99 chr9:35075324:35075324:T:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 35075324 35075324 T G snp splicing FANCG(NM_004629:exon12:c.1434-2A>C) splicing FANCG splice_acceptor_variant,NMD_transcript_variant splicing ENSG00000221829 PASS FALSE TRUE TRUE TRUE TRUE 4.47 0.000786164 ENSG00000221829(ENST00000425676:exon11:c.1231-2A>C,ENST00000378643:exon12:c.1434-2A>C) - - 22,0 23,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0255 99 chr9:35075954:35075954:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 35075954 35075954 C T snp splicing FANCG(NM_004629:exon10:c.1143+5G>A) splicing FANCG splice_region_variant,intron_variant,NMD_transcript_variant splicing ENSG00000221829 PASS FALSE TRUE TRUE TRUE TRUE 5.33 0.000786164 ENSG00000221829(ENST00000425676:exon9:c.940+5G>A,ENST00000378643:exon10:c.1143+5G>A) - - 26,0 21,0 0,0,145 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-03-0076 99 chr9:35076435:35076435:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 35076435 35076435 G A snp nonsynonymous SNV FANCG:NM_004629:exon8:c.C1070T:p.T357M, nonsynonymous SNV FANCG missense_variant nonsynonymous SNV ENSG00000221829 PASS FALSE TRUE TRUE TRUE TRUE -0.724 0.000784929 ENSG00000221829:ENST00000378643:exon8:c.C1070T:p.T357M, 357 T/M 23,0 23,0 0,0,146 0,1,490 0,0,145 0,1,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0237 99 chr9:35077331:35077331:A:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 35077331 35077331 A C snp nonsynonymous SNV FANCG:NM_004629:exon5:c.T576G:p.D192E, nonsynonymous SNV FANCG missense_variant nonsynonymous SNV ENSG00000221829 PASS FALSE TRUE TRUE TRUE TRUE 0.64 0.000786164 ENSG00000221829:ENST00000378643:exon5:c.T576G:p.D192E,ENSG00000221829:ENST00000448890:exon6:c.T576G:p.D192E, 192 D/E 89,0 31,0 0,0,145 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0392 99 chr9:35077451:35077451:C:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 35077451 35077451 C G snp intronic FANCG intronic FANCG intron_variant intronic ENSG00000221829 PASS FALSE TRUE TRUE TRUE TRUE 3.37 0.000787402 ENSG00000221829 - - 25,0 26,0 0,0,145 0,1,489 0,0,145 0,1,473 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0033 99 chr9:35079311:35079311:C:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 35079311 35079311 C A snp intronic FANCG intronic FANCG non_coding_exon_variant,nc_transcript_variant intronic ENSG00000221829 PASS FALSE TRUE TRUE TRUE TRUE 2.57 0.000787402 ENSG00000221829 - - 7,0 3,0 0,0,144 0,1,490 0,0,143 0,1,483 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0258 99 chr9:86616021:86616021:T:C:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr9 86616021 86616021 T C snp synonymous SNV RMI1:NM_024945:exon3:c.T120C:p.N40N, synonymous SNV RMI1 synonymous_variant synonymous SNV ENSG00000178966 PASS FALSE FALSE TRUE TRUE TRUE 4.2 0.00157233 ENSG00000178966:ENST00000445877:exon3:c.T120C:p.N40N,ENSG00000178966:ENST00000325875:exon3:c.T120C:p.N40N, 40 N 29,0 20,0 0,0,145 0,2,489 0,0,145 0,2,488 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0087,AOGC-02-0105 92,99 chr9:86616054:86616054:A:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 86616054 86616054 A G snp synonymous SNV RMI1:NM_024945:exon3:c.A153G:p.Q51Q, synonymous SNV RMI1 synonymous_variant synonymous SNV ENSG00000178966 PASS FALSE TRUE TRUE TRUE TRUE 5.86 0.000786164 ENSG00000178966:ENST00000445877:exon3:c.A153G:p.Q51Q,ENSG00000178966:ENST00000325875:exon3:c.A153G:p.Q51Q, 51 Q 29,0 20,0 0,1,144 0,0,491 0,1,144 0,0,489 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2838-03A-01W-0726-08 99 chr9:86616372:86616372:T:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 86616372 86616372 T G snp synonymous SNV RMI1:NM_024945:exon3:c.T471G:p.L157L, synonymous SNV RMI1 synonymous_variant synonymous SNV ENSG00000178966 PASS FALSE TRUE TRUE TRUE TRUE 3.4 0.000786164 ENSG00000178966:ENST00000445877:exon3:c.T471G:p.L157L,ENSG00000178966:ENST00000325875:exon3:c.T471G:p.L157L, 157 L 29,0 20,0 0,1,144 0,0,491 0,1,144 0,0,486 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2950-03A-01W-0733-08 99 chr9:86616443:86616443:T:C:snp 0.437132683329212 -0.232339089481946 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr9 86616443 86616443 T C snp nonsynonymous SNV RMI1:NM_024945:exon3:c.T542C:p.L181S, nonsynonymous SNV RMI1 missense_variant nonsynonymous SNV ENSG00000178966 PASS FALSE FALSE TRUE TRUE TRUE 5.76 0.00157233 ENSG00000178966:ENST00000445877:exon3:c.T542C:p.L181S,ENSG00000178966:ENST00000325875:exon3:c.T542C:p.L181S, 181 L/S 29,0 20,0 0,0,145 0,2,489 0,0,145 0,2,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0475,AOGC-03-0121 99,99 chr9:86616901:86616901:A:G:snp 0.27105525402704 -0.233070866141732 0.21176023297084 0.00312989045383412 0.00312989045383412 1 1 0 chr9 86616901 86616901 A G snp nonsynonymous SNV RMI1:NM_024945:exon3:c.A1000G:p.K334E, nonsynonymous SNV RMI1 missense_variant nonsynonymous SNV ENSG00000178966 PASS FALSE FALSE FALSE TRUE TRUE -3.21 0.00314961 ENSG00000178966:ENST00000445877:exon3:c.A1000G:p.K334E,ENSG00000178966:ENST00000325875:exon3:c.A1000G:p.K334E, 334 K/E 29,0 20,0 0,0,145 0,4,486 0,0,145 0,4,476 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0032,AOGC-02-0304,AOGC-03-0129,AOGC-08-0185 99,99,99,99 chr9:86616918:86616918:G:A:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr9 86616918 86616918 G A snp synonymous SNV RMI1:NM_024945:exon3:c.G1017A:p.L339L, synonymous SNV RMI1 synonymous_variant synonymous SNV ENSG00000178966 PASS FALSE TRUE TRUE TRUE TRUE 2.52 0.00157729 ENSG00000178966:ENST00000445877:exon3:c.G1017A:p.L339L,ENSG00000178966:ENST00000325875:exon3:c.G1017A:p.L339L, 339 L 29,0 20,0 0,1,144 0,1,488 0,1,144 0,0,476 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2821-03B-01W-0728-08 99 AOGC-08-0064 54 chr9:86617489:86617489:A:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 86617489 86617489 A G snp nonsynonymous SNV RMI1:NM_024945:exon3:c.A1588G:p.I530V, nonsynonymous SNV RMI1 missense_variant nonsynonymous SNV ENSG00000178966 PASS FALSE FALSE TRUE TRUE TRUE -6.37 0.000786164 ENSG00000178966:ENST00000325875:exon3:c.A1588G:p.I530V, 530 I/V 23,0 25,0 0,1,144 0,0,491 0,1,144 0,0,489 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2858-03D-01W-0755-09 99 chr9:86617595:86617595:A:G:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 86617595 86617595 A G snp nonsynonymous SNV RMI1:NM_024945:exon3:c.A1694G:p.K565R, nonsynonymous SNV RMI1 missense_variant nonsynonymous SNV ENSG00000178966 PASS FALSE TRUE TRUE TRUE TRUE 4.59 0.000787402 ENSG00000178966:ENST00000325875:exon3:c.A1694G:p.K565R, 565 K/R 23,0 25,0 0,0,145 0,1,489 0,0,145 0,1,488 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0252 85 chr9:97864059:97864059:A:G:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 97864059 97864059 A G snp nonsynonymous SNV FANCC:NM_000136:exon15:c.T1607C:p.L536P,FANCC:NM_001243743:exon15:c.T1607C:p.L536P, nonsynonymous SNV FANCC missense_variant nonsynonymous SNV ENSG00000158169 PASS TRUE TRUE TRUE TRUE TRUE 3.56 0.000789889 ENSG00000158169:ENST00000375305:exon15:c.T1607C:p.L536P,ENSG00000158169:ENST00000289081:exon15:c.T1607C:p.L536P, 536 L/P 22,0 23,0 0,1,144 0,0,488 0,1,143 0,0,463 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2911-03A-01W-0732-08 99 chr9:97864063:97864063:G:A:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 97864063 97864063 G A snp nonsynonymous SNV FANCC:NM_000136:exon15:c.C1603T:p.R535C,FANCC:NM_001243743:exon15:c.C1603T:p.R535C, nonsynonymous SNV FANCC missense_variant nonsynonymous SNV ENSG00000158169 PASS FALSE FALSE TRUE TRUE TRUE 4.76 0.000789889 ENSG00000158169:ENST00000375305:exon15:c.C1603T:p.R535C,ENSG00000158169:ENST00000289081:exon15:c.C1603T:p.R535C, 535 R/C 22,0 23,0 0,0,145 0,1,487 0,0,144 0,1,459 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0234 99 chr9:97873912:97873912:C:A:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 97873912 97873912 C A snp stopgain SNV FANCC:NM_000136:exon13:c.G1162T:p.G388X,FANCC:NM_001243743:exon13:c.G1162T:p.G388X,FANCC:NM_001243744:exon13:c.G1162T:p.G388X, stopgain SNV FANCC stop_gained stopgain SNV ENSG00000158169 PASS TRUE TRUE TRUE TRUE TRUE -1.59 0.000787402 ENSG00000158169:ENST00000375305:exon13:c.G1162T:p.G388X,ENSG00000158169:ENST00000289081:exon13:c.G1162T:p.G388X, 388 G/* 26,0 20,0 0,1,144 0,0,490 0,1,144 0,0,458 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2870-03A-01W-0732-08 99 chr9:97887430:97887430:T:C:snp 0.367893462920345 0.26923076923077 0.299003691665853 0.00156494522691706 0.00156494522691706 1 1 0 chr9 97887430 97887430 T C snp nonsynonymous SNV FANCC:NM_000136:exon10:c.A934G:p.I312V,FANCC:NM_001243743:exon10:c.A934G:p.I312V,FANCC:NM_001243744:exon10:c.A934G:p.I312V, nonsynonymous SNV FANCC missense_variant nonsynonymous SNV ENSG00000158169 PASS FALSE FALSE TRUE TRUE TRUE -1.29 0.00157233 ENSG00000158169:ENST00000375305:exon10:c.A934G:p.I312V,ENSG00000158169:ENST00000289081:exon10:c.A934G:p.I312V, 312 I/V 25,0 24,0 0,1,144 0,1,490 0,1,144 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2863-03B-01W-0728-08 99 AOGC-03-0123 99 chr9:97897645:97897645:T:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 97897645 97897645 T C snp nonsynonymous SNV FANCC:NM_000136:exon8:c.A826G:p.I276V,FANCC:NM_001243743:exon8:c.A826G:p.I276V,FANCC:NM_001243744:exon8:c.A826G:p.I276V, nonsynonymous SNV FANCC missense_variant nonsynonymous SNV ENSG00000158169 PASS FALSE FALSE TRUE TRUE TRUE -1.77 0.000786164 ENSG00000158169:ENST00000375305:exon8:c.A826G:p.I276V,ENSG00000158169:ENST00000289081:exon8:c.A826G:p.I276V, 276 I/V 21,0 22,0 0,0,145 0,1,490 0,0,145 0,1,487 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0335 99 chr9:97912259:97912259:G:C:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 97912259 97912259 G C snp nonsynonymous SNV FANCC:NM_000136:exon7:c.C632G:p.P211R,FANCC:NM_001243743:exon7:c.C632G:p.P211R,FANCC:NM_001243744:exon7:c.C632G:p.P211R, nonsynonymous SNV FANCC missense_variant nonsynonymous SNV ENSG00000158169 PASS FALSE FALSE TRUE TRUE TRUE 3.87 0.000784929 ENSG00000158169:ENST00000375305:exon7:c.C632G:p.P211R,ENSG00000158169:ENST00000289081:exon7:c.C632G:p.P211R, 211 P/R 22,0 17,0 0,0,146 0,1,490 0,0,145 0,1,490 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-08-0051 99 chr9:97912307:97912307:T:A:snp 0.866515946988662 -0.0318611987381696 0.189553423814011 0.00391236306729264 0.00391236306729264 1 1 0 chr9 97912307 97912307 T A snp nonsynonymous SNV FANCC:NM_000136:exon7:c.A584T:p.D195V,FANCC:NM_001243743:exon7:c.A584T:p.D195V,FANCC:NM_001243744:exon7:c.A584T:p.D195V, nonsynonymous SNV FANCC missense_variant nonsynonymous SNV ENSG00000158169 PASS FALSE FALSE TRUE TRUE TRUE 4.77 0.00392465 ENSG00000158169:ENST00000375305:exon7:c.A584T:p.D195V,ENSG00000158169:ENST00000289081:exon7:c.A584T:p.D195V, 195 D/V 22,0 21,0 0,1,145 0,4,487 0,1,144 0,4,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2841-03B-01W-0728-08 99 AOGC-02-0105,AOGC-02-0106,AOGC-02-0108,AOGC-03-0152 99,91,99,99 chr9:98009786:98009786:C:T:snp 0.582990036209495 -0.231974921630093 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 98009786 98009786 C T snp nonsynonymous SNV FANCC:NM_000136:exon3:c.G178A:p.V60I,FANCC:NM_001243743:exon3:c.G178A:p.V60I,FANCC:NM_001243744:exon3:c.G178A:p.V60I, nonsynonymous SNV FANCC missense_variant nonsynonymous SNV ENSG00000158169 PASS FALSE FALSE TRUE TRUE TRUE -5.4 0.000784929 ENSG00000158169:ENST00000433829:exon3:c.G178A:p.V60I,ENSG00000158169:ENST00000375305:exon3:c.G178A:p.V60I,ENSG00000158169:ENST00000289081:exon3:c.G178A:p.V60I, 60 V/I 22,0 23,0 0,0,146 0,1,490 0,0,145 0,1,483 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 AOGC-02-0302 99 chr9:98011461:98011461:A:C:snp 0.068543172725465 0.769592476489029 0.422523554870793 0.000782472613458529 0.000782472613458529 1 1 0 chr9 98011461 98011461 A C snp nonsynonymous SNV FANCC:NM_000136:exon2:c.T113G:p.V38G,FANCC:NM_001243743:exon2:c.T113G:p.V38G,FANCC:NM_001243744:exon2:c.T113G:p.V38G, nonsynonymous SNV FANCC missense_variant nonsynonymous SNV ENSG00000158169 PASS TRUE TRUE TRUE TRUE TRUE 5.13 0.000784929 ENSG00000158169:ENST00000433829:exon2:c.T113G:p.V38G,ENSG00000158169:ENST00000375305:exon2:c.T113G:p.V38G,ENSG00000158169:ENST00000289081:exon2:c.T113G:p.V38G, 38 V/G 20,0 20,0 0,1,145 0,0,491 0,1,145 0,0,485 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2914-03A-01W-0732-08 99 chr9:98011497:98011497:G:A:snp 0.320420066787549 -0.133704292527821 0.134566185463994 0.00782472613458529 0.00782472613458529 1 1 0 chr9 98011497 98011497 G A snp nonsynonymous SNV FANCC:NM_000136:exon2:c.C77T:p.S26F,FANCC:NM_001243743:exon2:c.C77T:p.S26F,FANCC:NM_001243744:exon2:c.C77T:p.S26F, nonsynonymous SNV FANCC missense_variant nonsynonymous SNV ENSG00000158169 PASS FALSE FALSE FALSE TRUE TRUE 4.22 0.00784929 ENSG00000158169:ENST00000433829:exon2:c.C77T:p.S26F,ENSG00000158169:ENST00000375305:exon2:c.C77T:p.S26F,ENSG00000158169:ENST00000289081:exon2:c.C77T:p.S26F, 26 S/F 20,0 20,0 0,1,145 0,9,482 0,1,145 0,9,480 1 1 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2806-03B-01W-0728-08 99 AOGC-02-0096,AOGC-02-0284,AOGC-03-0001,AOGC-03-0121,AOGC-03-0142,AOGC-05-0020,AOGC-08-0006,AOGC-08-0064,AOGC-08-0068 99,99,99,99,99,99,76,99,99 chr9:98009614:98009614:A:-:indel 0.734989807319422 0.0303500846979116 0.0896617044196647 0.0179968701095462 0.0179968701095462 1 1 0 chr9 98009614 98009614 A - indel intronic FANCC intronic FANCC intron_variant,feature_truncation intronic ENSG00000158169 PASS TRUE TRUE TRUE TRUE TRUE 2.1 0.0183121 ENSG00000158169 - - 7,0 7,0 0,6,138 0,17,467 0,6,137 0,14,401 1 0 1 1 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 1 TCGA-AB-2824-03B-01W-0728-08,TCGA-AB-2847-03B-01W-0728-08,TCGA-AB-2859-03B-01W-0728-08,TCGA-AB-2868-03B-01W-0728-08,TCGA-AB-2883-03A-01W-0732-08,TCGA-AB-2945-03A-01W-0733-08 9,17,34,14,28,41 AOGC-02-0112,AOGC-02-0144,AOGC-02-0289,AOGC-02-0306,AOGC-02-0358,AOGC-02-0528,AOGC-03-0047,AOGC-03-0087,AOGC-05-0020,AOGC-08-0019,AOGC-08-0128,AOGC-08-0192,AOGC-08-0218,AOGC-08-0247,AOGC-08-0286,AOGC-08-0302,AOGC-14-0425 26,23,50,30,35,23,29,38,32,36,24,12,2,45,23,29,38