Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_position End_position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID COSMIC_Codon COSMIC_Gene Transcript_Id Exon ChromChange AAChange Genome_Plus_Minus_10_Bp Drug_Target TTotCov TVarCov NTotCov NVarCov dbSNPPopFreq COSMIC_Gene_Freq COSMIC_Site_Freq TVarRat NVarRat dbSNP_Strength dbSNP_AF dbSNP_PopFreq Confidence Algorithm PRAMEF12 390999 hgsc.bcm.edu hg19 1 12835275 12835275 + Missense_Mutation SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . PRAMEF12 NM_001080830 exon1 c.C265T p.L89F GCACTGCTTGCCC . 83.0 25.0 74.0 0.0 . 69 . . . none . . PASS Atlas-SNP RPE65 6121 hgsc.bcm.edu hg19 1 68910320 68910320 + Missense_Mutation SNP T T A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . RPE65 NM_000329 exon5 c.A389T p.D130V GCATTGTCAGTAA . 126.0 28.0 134.0 0.0 . 87 . . . none . . PASS Atlas-SNP CENPF 1063 hgsc.bcm.edu hg19 1 214802436 214802436 + Silent SNP T T C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . CENPF NM_016343 exon8 c.T1116C p.S372S TTTGAGTTGTCAG . 340.0 14.0 301.0 0.0 . 321 . . . none . . PASS Atlas-SNP LBR 3930 hgsc.bcm.edu hg19 1 225592163 225592163 + Missense_Mutation SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . LBR NM_194442 exon13 c.C1630T p.R544C GGTGGCGAACAAA . 118.0 13.0 133.0 0.0 . 54 . . . none . . PASS Atlas-SNP OTOF 9381 hgsc.bcm.edu hg19 2 26781380 26781380 + Silent SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . OTOF NM_194248 exon1 c.C60T p.I20I TTTGGCGATCCGG . 164.0 39.0 172.0 0.0 . 524 . . . none . . PASS Atlas-SNP OTOF 9381 hgsc.bcm.edu hg19 2 26781388 26781388 + Missense_Mutation SNP C C A rs376856990 alternate_allele TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . OTOF NM_194248 exon1 c.G52T p.D18Y TCCGGTCGCCCCT . 160.0 37.0 165.0 0.0 . 524 . . . alt . . PASS Atlas-SNP DCLK3 85443 hgsc.bcm.edu hg19 3 36779671 36779671 + Silent SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . DCLK3 NM_033403 exon2 c.G480A p.G160G ACTGGTCCCCAGA . 160.0 27.0 142.0 0.0 . 95 . . . none . . PASS Atlas-SNP SCN11A 11280 hgsc.bcm.edu hg19 3 38908836 38908836 + Silent SNP G G A rs371852759 TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . SCN11A NM_014139 exon23 c.C3927T p.D1309D GAAGTTGTCAATG . 86.0 21.0 92.0 0.0 . 296 . . . weak . . PASS Atlas-SNP C5orf42 65250 hgsc.bcm.edu hg19 5 37185181 37185181 + Missense_Mutation SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . C5orf42 NM_023073 exon25 c.G4190A p.G1397E TGGGGTCCTGGAA . 193.0 47.0 191.0 0.0 . 422 . . . none . . PASS Atlas-SNP CCNO 10309 hgsc.bcm.edu hg19 5 54528321 54528321 + Silent SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . CCNO NM_021147 exon2 c.C435T p.R145R GAATTGGCGGTGC . 204.0 43.0 162.0 0.0 . 17 . . . none . . PASS Atlas-SNP MAS1L 116511 hgsc.bcm.edu hg19 6 29455103 29455103 + Missense_Mutation SNP C C G novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . MAS1L NM_052967 exon1 c.G577C p.V193L TGCAGACAACATT . 127.0 10.0 111.0 0.0 . 66 . . . none . . PASS Atlas-SNP CASP8AP2 9994 hgsc.bcm.edu hg19 6 90573481 90573481 + Missense_Mutation SNP A A G novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . CASP8AP2 NM_001137667 exon7 c.A2053G p.M685V TCTCCTATGGAAA . 110.0 25.0 86.0 0.0 . 108 . . . none . . PASS Atlas-SNP COQ3 51805 hgsc.bcm.edu hg19 6 99817502 99817502 + Missense_Mutation SNP C C A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . COQ3 NM_017421 exon7 c.G1084T p.A362S GCACAGCTGGATT . 181.0 41.0 169.0 0.0 . 19 . . . none . . PASS Atlas-SNP TNRC18 84629 hgsc.bcm.edu hg19 7 5414035 5414035 + Missense_Mutation SNP C C G novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . TNRC18 NM_001080495 exon10 c.G2880C p.K960N GCCAGCCTTGCCC . 50.0 16.0 28.0 0.0 . 311 . . . none . . PASS Atlas-SNP VWC2 375567 hgsc.bcm.edu hg19 7 49815638 49815638 + Missense_Mutation SNP G G C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . VWC2 NM_198570 exon2 c.G607C p.D203H CACGTCGACACGA . 28.0 16.0 17.0 0.0 . 30 . . . none . . PASS Atlas-SNP FAM83A 84985 hgsc.bcm.edu hg19 8 124206353 124206353 + Silent SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . FAM83A NM_032899 exon3 c.C738T p.I246I CATCATCTCGGAC . 64.0 15.0 59.0 0.0 . 64 . . . none . . PASS Atlas-SNP HNRNPH3 3189 hgsc.bcm.edu hg19 10 70098907 70098907 + Silent SNP T T C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . HNRNPH3 NM_012207 exon5 c.T447C p.G149G TGGAGGTTTTGAT . 131.0 38.0 123.0 0.0 . 33 . . . none . . PASS Atlas-SNP PLAC9 219348 hgsc.bcm.edu hg19 10 81901918 81901918 + Missense_Mutation SNP C C G novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . PLAC9 NM_001012973 exon2 c.C145G p.L49V CGCCGTCTAGATG . 44.0 10.0 28.0 0.0 . 9 . . . none . . PASS Atlas-SNP SORCS1 114815 hgsc.bcm.edu hg19 10 108427453 108427453 + Missense_Mutation SNP C C A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . SORCS1 NM_001206572 exon17 c.G2297T p.S766I CCAGTACTATTGA . 65.0 15.0 52.0 0.0 . 534 . . . none . . PASS Atlas-SNP CSTF3 1479 hgsc.bcm.edu hg19 11 33163206 33163206 + Missense_Mutation SNP T T C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . CSTF3 NM_001033505 exon3 c.A232G p.I78V ATAAAATAGTAAC . 147.0 9.0 119.0 0.0 . 59 . . . none . . PASS Atlas-SNP GLYATL1 92292 hgsc.bcm.edu hg19 11 58723454 58723454 + Missense_Mutation SNP A A G novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . GLYATL1 NM_080661 exon7 c.A956G p.E319G CCTGTGAGTGGCA . 108.0 23.0 67.0 0.0 . 89 . . . none . . PASS Atlas-SNP MS4A8 83661 hgsc.bcm.edu hg19 11 60470856 60470856 + Silent SNP C C A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . . NM_031457 exon3 c.C225A p.I75I GGCCATCCAGATC . 160.0 17.0 141.0 0.0 . . . . . none . . PASS Atlas-SNP TMEM134 80194 hgsc.bcm.edu hg19 11 67232160 67232160 + Silent SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . TMEM134 NM_025124 exon7 c.C513T p.H171H GATCACGTGATAG . 105.0 6.0 82.0 0.0 . 4 . . . none . . PASS Atlas-SNP ITPR2 3709 hgsc.bcm.edu hg19 12 26639109 26639109 + Silent SNP G G C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . ITPR2 NM_002223 exon41 c.C5739G p.P1913P AATTGCGGGACTC . 577.0 32.0 437.0 0.0 . 270 . . . none . . PASS Atlas-SNP USP30 84749 hgsc.bcm.edu hg19 12 109520853 109520853 + Missense_Mutation SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . USP30 NM_032663 exon11 c.G1154A p.G385E GGCCGGGAGCCCC . 96.0 7.0 59.0 0.0 . 48 . . . none . . PASS Atlas-SNP FLT3 2322 hgsc.bcm.edu hg19 13 28624244 28624244 + Missense_Mutation SNP G G C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . FLT3 NM_004119 exon6 c.C730G p.L244V TGAACAGCCTGGT . 137.0 35.0 113.0 0.0 . 15525 . . . none . . PASS Atlas-SNP G2E3 55632 hgsc.bcm.edu hg19 14 31061654 31061654 + Splice_Site SNP G G C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . G2E3 NM_017769 exon5 c.362+1G>C . TTTTGCGTGAGTT . 146.0 28.0 121.0 0.0 . 82 . . . none . . PASS Atlas-SNP CEP128 145508 hgsc.bcm.edu hg19 14 81297497 81297497 + Nonsense_Mutation SNP G G T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 CEP128,NS,carcinoma,0,1 CEP128 NM_152446 exon12 c.C1199A p.S400X ACTTGTGATGCCA . 215.0 43.0 188.0 0.0 . 146 . . . none . . PASS Atlas-SNP FAM181A 90050 hgsc.bcm.edu hg19 14 94395093 94395093 + Silent SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . FAM181A NM_138344 exon3 c.G648A p.E216E GCTGGAGGGGGGA . 53.0 11.0 27.0 0.0 . 42 . . . none . . PASS Atlas-SNP ZNF839 55778 hgsc.bcm.edu hg19 14 102805492 102805492 + Missense_Mutation SNP C C A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . ZNF839 NM_018335 exon7 c.C1859A p.T620N ACGATACCACTGA . 118.0 28.0 102.0 0.0 . 41 . . . none . . PASS Atlas-SNP OR4M2 390538 hgsc.bcm.edu hg19 15 22369316 22369316 + Silent SNP C C G novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . OR4M2 NM_001004719 exon1 c.C741G p.T247T CATTACCATTGTG . 399.0 57.0 336.0 0.0 . 140 . . . none . . PASS Atlas-SNP CEP152 22995 hgsc.bcm.edu hg19 15 49030644 49030644 + Silent SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 CEP152,NS,carcinoma,0,1 CEP152 NM_001194998 exon27 c.G4935A p.T1645T CAAATACGTGGTT . 215.0 40.0 200.0 0.0 . 145 . . . none . . PASS Atlas-SNP TRPM7 54822 hgsc.bcm.edu hg19 15 50978726 50978726 + Splice_Site SNP A A G novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . TRPM7 NM_017672 exon2 c.3+2T>C . TCCAGTACCATTC . 46.0 10.0 44.0 0.0 . 145 . . . none . . PASS Atlas-SNP UNKL 64718 hgsc.bcm.edu hg19 16 1442978 1442978 + Splice_Site SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . UNKL NM_001193388 exon9 c.938-1G>A . GGCTCTCTGCAAG . 57.0 10.0 55.0 0.0 . 46 . . . none . . PASS Atlas-SNP TNRC6A 27327 hgsc.bcm.edu hg19 16 24801625 24801625 + Silent SNP C C G rs377201148 alternate_allele TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . TNRC6A NM_014494 exon6 c.C1662G p.G554G GCCTGGCGTAAAT . 124.0 29.0 115.0 0.0 . 171 . . . alt . . PASS Atlas-SNP SMARCE1 6605 hgsc.bcm.edu hg19 17 38793826 38793826 + Splice_Site SNP T T C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . SMARCE1 NM_003079 exon6 c.157-2A>G . GATGCCTACGAAA . 118.0 49.0 75.0 0.0 . 34 . . . none . . PASS Atlas-SNP GPS1 2873 hgsc.bcm.edu hg19 17 80013100 80013100 + Splice_Site SNP T T C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . GPS1 NM_004127 exon6 c.760+2T>C . CGCAGGTGAGGGC . 114.0 18.0 88.0 0.0 . 30 . . . none . . PASS Atlas-SNP CCDC57 284001 hgsc.bcm.edu hg19 17 80156212 80156212 + Missense_Mutation SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . CCDC57 NM_198082 exon3 c.G494A p.G165D AGCTCACCGTCGA . 172.0 32.0 130.0 0.0 . 102 . . . none . . PASS Atlas-SNP MUC16 94025 hgsc.bcm.edu hg19 19 9016700 9016700 + Silent SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . MUC16 NM_024690 exon28 c.C38037T p.D12679D CCCAAGGTCCACT . 89.0 24.0 97.0 0.0 . 4315 . . . none . . PASS Atlas-SNP MUC16 94025 hgsc.bcm.edu hg19 19 9075870 9075870 + Missense_Mutation SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . MUC16 NM_024690 exon3 c.C11576T p.T3859I TCTGTTGTAAGAG . 167.0 43.0 157.0 0.0 . 4315 . . . none . . PASS Atlas-SNP GCDH 2639 hgsc.bcm.edu hg19 19 13002330 13002330 + Silent SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . GCDH NM_013976 exon3 c.A121A p.R41R CAACTGGCTAAGT . 68.0 13.0 55.0 0.0 . 76 . . . none . . PASS Atlas-SNP ZBTB32 27033 hgsc.bcm.edu hg19 19 36206193 36206193 + Missense_Mutation SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . ZBTB32 NM_014383 exon2 c.C665T p.S222F GGGGCTCTGAGGA . 19.0 7.0 20.0 0.0 . 33 . . . none . . PASS Atlas-SNP SRRM5 100170229 hgsc.bcm.edu hg19 19 44118259 44118259 + Silent SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . SRRM5 NM_001145641 exon1 c.C1986T p.L662L CAGTCTCAGTCAG . 39.0 12.0 32.0 0.0 . 38 . . . none . . PASS Atlas-SNP BAX 581 hgsc.bcm.edu hg19 19 49459013 49459013 + Missense_Mutation SNP G G T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . BAX NM_004324 exon3 c.G156T p.Q52H GCCTCAGGATGCG . 116.0 37.0 97.0 0.0 . 69 . . . none . . PASS Atlas-SNP TTYH1 57348 hgsc.bcm.edu hg19 19 54946848 54946848 + Missense_Mutation SNP G G T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . TTYH1 NM_020659 exon11 c.G1252T p.A418S GCCTGGGCCCTCT . 108.0 38.0 85.0 0.0 . 78 . . . none . . PASS Atlas-SNP MMP24 10893 hgsc.bcm.edu hg19 20 33862094 33862094 + Missense_Mutation SNP G G T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . MMP24 NM_006690 exon9 c.G1620T p.K540N CTACAAGGGCCGG . 32.0 11.0 15.0 0.0 . 35 . . . none . . PASS Atlas-SNP KREMEN1 83999 hgsc.bcm.edu hg19 22 29533423 29533423 + Missense_Mutation SNP G G C novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . KREMEN1 NM_001039570 exon6 c.G725C p.C242S GGGTCTGCTACTG . 169.0 29.0 111.0 0.0 . 46 . . . none . . PASS Atlas-SNP CABP7 164633 hgsc.bcm.edu hg19 22 30123661 30123661 + Missense_Mutation SNP G G T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . CABP7 NM_182527 exon2 c.G120T p.E40D CCGAGAGGCCTTC . 56.0 9.0 44.0 0.0 . 9 . . . none . . PASS Atlas-SNP TMEM184B 25829 hgsc.bcm.edu hg19 22 38621517 38621517 + Missense_Mutation SNP A A G novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . TMEM184B NM_001195071 exon7 c.T701C p.F234S GTGGCGAAGTAGA . 52.0 8.0 33.0 0.0 . 19 . . . none . . PASS Atlas-SNP MXRA5 25878 hgsc.bcm.edu hg19 X 3229194 3229194 + Missense_Mutation SNP G G T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . MXRA5 NM_015419 exon7 c.C7050A p.N2350K AGTCTTGTTCCGG . 38.0 4.0 37.0 0.0 . 815 . . . none . . PASS Atlas-SNP AR 367 hgsc.bcm.edu hg19 X 66765167 66765167 + Missense_Mutation SNP A A T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . AR NM_000044 exon1 c.A179T p.Q60L AGCAGCAGCAGCA . 48.0 6.0 34.0 0.0 . 249 . . . none . . PASS Atlas-SNP STAG2 10735 hgsc.bcm.edu hg19 X 123229293 123229293 + Missense_Mutation SNP T T A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 T T . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . STAG2 NM_001042749 exon34 c.T3777A p.D1259E TATGGATGAATCA . 134.0 24.0 142.0 0.0 . 309 . . . none . . PASS Atlas-SNP MAGEA4 4103 hgsc.bcm.edu hg19 X 151092975 151092975 + Missense_Mutation SNP C C T novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . MAGEA4 NM_001011548 exon3 c.C839T p.A280V CTCTGGCTGAAAC . 85.0 46.0 67.0 0.0 . 68 . . . none . . PASS Atlas-SNP COX1 5742 hgsc.bcm.edu hg19 MT 6853 6853 + Missense_Mutation SNP G G A novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . . ENST00000361624 exon1 c.G950A p.G317D CCACCGGCGTCAA . 41.0 12.0 24.0 0.0 . . . . . none . . PASS Atlas-SNP COX3 5742 hgsc.bcm.edu hg19 MT 9819 9819 + Nonsense_Mutation SNP G G A rs2854139 bycluster;byfrequency;alternate_allele TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 G G . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . . ENST00000362079 exon1 c.G613A p.G205X TTCCACGGACTTC . 37.0 6.0 25.0 0.0 . . . . . alt C|0.931;T|0.069 . PASS Atlas-SNP KRTAP5-7 440050 hgsc.bcm.edu hg19 11 71238734 71238760 + In_Frame_Del DEL TGCTGCTGTTCCTCAGGCTGTGGGTCA TGCTGCTGTTCCTCAGGCTGTGGGTCA - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 TGCTGCTGTTCCTCAGGCTGTGGGTCA TGCTGCTGTTCCTCAGGCTGTGGGTCA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . KRTAP5-7 NM_001012503 exon1 c.387_413del p.129_138del . . 117.0 12.0 89.0 0.0 . 23 . 0.102564 0 none . . PASS Atlas-INDEL EPS15L1 58513 hgsc.bcm.edu hg19 19 16545212 16545214 + In_Frame_Del DEL GAG GAG - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 GAG GAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . EPS15L1 NM_021235 exon7 c.461_463del p.154_155del . . 61.0 11.0 83.0 0.0 . 81 . 0.180328 0 none . . PASS Atlas-Indel,Pindel C11orf94 143678 hgsc.bcm.edu hg19 11 45928455 45928456 + Frame_Shift_Ins INS - - G novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 - - . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . C11orf94 NM_001080446 exon2 c.140_141insC p.L47fs . . 57.0 12.0 37.0 0.0 . 13 . 0.210526 0 none . . PASS Atlas-Indel,Pindel AFG3L2 10939 hgsc.bcm.edu hg19 18 12359961 12359965 + Frame_Shift_Del DEL ATTTT ATTTT - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 ATTTT ATTTT . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . AFG3L2 NM_006796 exon7 c.714_718del p.238_240del . . 123.0 14.0 100.0 0.0 . 60 . 0.113821 0 none . . PASS Atlas-Indel,Pindel RPE65 6121 hgsc.bcm.edu hg19 1 68910331 68910343 + Frame_Shift_Del DEL TACTCCTCGAAAG TACTCCTCGAAAG - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 TACTCCTCGAAAG TACTCCTCGAAAG . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . RPE65 NM_000329 exon5 c.367_379del p.123_127del . . 116.0 24.0 128.0 0.0 . 87 . 0.206897 0 none . . PASS Atlas-Indel,Pindel OR1E1 8387 hgsc.bcm.edu hg19 17 3301172 3301172 + Frame_Shift_Del DEL A A - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . OR1E1 NM_003553 exon1 c.534delC p.F178fs . . 156.0 59.0 106.0 0.0 . 37 . 0.378205 0 none . . PASS Atlas-Indel,Pindel SCN11A 11280 hgsc.bcm.edu hg19 3 38908838 38908838 + Frame_Shift_Del DEL C C - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 C C . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . SCN11A NM_014139 exon23 c.3926delA p.D1309fs . . 87.0 21.0 94.0 0.0 . 296 . 0.241379 0 none . . PASS Atlas-INDEL SCFD2 152579 hgsc.bcm.edu hg19 4 54140020 54140020 + Frame_Shift_Del DEL A A - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 A A . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . SCFD2 NM_152540 exon4 c.1285delC p.L429fs . . 93.0 18.0 80.0 0.0 . 78 . 0.193548 0 none . . PASS Atlas-Indel,Pindel MAP2K7 5609 hgsc.bcm.edu hg19 19 7975668 7975757 + Frame_Shift_Del DEL CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA CTGGGCAAGATGACAGTGGCGGTGAGTGACCAGGCGGGGCTTGCACTGGGCAGGATGACAGAGGCGGTGAGTGACCAGGCGGGGCGTGCA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . MAP2K7 NM_145185 exon6 c.654_675del p.218_225del . . 56.0 18.0 65.0 0.0 . 66 . 0.321 . none . . PASS Pindel SCN11A 11280 hgsc.bcm.edu hg19 3 38908836 38908839 + Frame_Shift_Del DEL GTCA GTCA - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 GTCA GTCA . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . SCN11A NM_014139 exon23 c.3925_3928del p.1309_1310del . . 88.0 18.0 93.0 0.0 . 296 . 0.205 . none . . PASS Pindel KRT72 140807 hgsc.bcm.edu hg19 12 52981529 52981549 + In_Frame_Del DEL GCCTGGTGCAGGGCGCCCTCC GCCTGGTGCAGGGCGCCCTCC - novel TCGA-IA-A83T-01A-11D-A34Z-10 TCGA-IA-A83T-11A-11D-A34Z-10 GCCTGGTGCAGGGCGCCCTCC GCCTGGTGCAGGGCGCCCTCC . . . . Unknown Untested Somatic PhaseI WXS none . . Illumina HiSeq 580ff01c-dd91-46ed-a426-7b2afea92207 cfd3629b-47b9-4934-86ab-9695c9f95668 . KRT72 NM_001146225 exon7 c.1177_1197del p.393_399del . . 128.0 12.0 103.0 0.0 . 70 . 0.094 . none . . PASS Pindel