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 dataset type classification start end gene chr ref_allele tum_allele1 tum_allele2 context IGSF21 84966 broad.mit.edu 36 1 18575958 18575958 + Silent SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 18575958 18575958 IGSF21 1 C C T 19 NBL1 4681 broad.mit.edu 36 1 19854233 19854233 + Silent SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 19854233 19854233 NBL1 1 C C T 22 RLF 6018 broad.mit.edu 36 1 40476178 40476178 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40476178 40476178 RLF 1 A A G 9 ERI3 79033 broad.mit.edu 36 1 44577347 44577347 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44577347 44577347 ERI3 1 A A G 7 DAB1 1600 broad.mit.edu 36 1 57249422 57249422 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 57249422 57249422 DAB1 1 C C A 28 DCST2 127579 broad.mit.edu 36 1 153272231 153272231 + Silent SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 153272231 153272231 DCST2 1 G G A 39 PPP1R12B 4660 broad.mit.edu 36 1 200731221 200731221 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 200731221 200731221 PPP1R12B 1 A A T 4 MIA3 375056 broad.mit.edu 36 1 220868349 220868349 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 220868349 220868349 MIA3 1 C C G 32 KIAA0913 23053 broad.mit.edu 36 10 75227155 75227155 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 75227155 75227155 KIAA0913 10 G G C 45 ECHS1 1892 broad.mit.edu 36 10 135030489 135030489 + Splice_Site_SNP SNP T T A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 135030489 135030489 ECHS1 10 T T A 55 PTPRJ 5795 broad.mit.edu 36 11 48103233 48103233 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 48103233 48103233 PTPRJ 11 G G A 47 MYO7A 4647 broad.mit.edu 36 11 76547025 76547025 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 76547025 76547025 MYO7A 11 C C T 23 KIAA1377 57562 broad.mit.edu 36 11 101320316 101320316 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 101320316 101320316 KIAA1377 11 G G A 40 HOXC6 3223 broad.mit.edu 36 12 52709744 52709744 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52709744 52709744 HOXC6 12 A A C 12 XRCC6BP1 91419 broad.mit.edu 36 12 56627075 56627075 + Silent SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 56627075 56627075 XRCC6BP1 12 C C T 27 USP15 9958 broad.mit.edu 36 12 61071288 61071288 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 61071288 61071288 USP15 12 A A C 12 ANO4 121601 broad.mit.edu 36 12 100014529 100014529 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 100014529 100014529 ANO4 12 C C T 17 MYL2 4633 broad.mit.edu 36 12 109841372 109841372 + Silent SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 109841372 109841372 MYL2 12 C C T 32 SERPINA3 12 broad.mit.edu 36 14 94155545 94155545 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 94155545 94155545 SERPINA3 14 T T C 54 BDKRB2 624 broad.mit.edu 36 14 95777005 95777005 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 95777005 95777005 BDKRB2 14 G G A 39 FANCI 55215 broad.mit.edu 36 15 87634458 87634458 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 87634458 87634458 FANCI 15 A A G 12 ZSCAN10 84891 broad.mit.edu 36 16 3079671 3079671 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3079671 3079671 ZSCAN10 16 G G A 38 SLC6A2 6530 broad.mit.edu 36 16 54248135 54248135 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54248135 54248135 SLC6A2 16 G G T 44 HYDIN 54768 broad.mit.edu 36 16 69561950 69561950 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 69561950 69561950 HYDIN 16 C C G 29 LIG3 3980 broad.mit.edu 36 17 30350453 30350453 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 30350453 30350453 LIG3 17 A A G 4 NAGLU 4669 broad.mit.edu 36 17 37949014 37949014 + Silent SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 37949014 37949014 NAGLU 17 G G A 39 DNAI2 64446 broad.mit.edu 36 17 69813052 69813052 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 69813052 69813052 DNAI2 17 C C T 21 SMCHD1 23347 broad.mit.edu 36 18 2687985 2687985 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2687985 2687985 SMCHD1 18 C C T 29 FHOD3 80206 broad.mit.edu 36 18 32594639 32594639 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32594639 32594639 FHOD3 18 C C T 27 PDCD5 9141 broad.mit.edu 36 19 37768650 37768650 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37768650 37768650 PDCD5 19 G G C 33 ZNF586 54807 broad.mit.edu 36 19 62982966 62982966 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 62982966 62982966 ZNF586 19 C C T 24 APOB 338 broad.mit.edu 36 2 21079001 21079001 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21079001 21079001 APOB 2 G G C 33 C2orf39 92749 broad.mit.edu 36 2 26500757 26500757 + Silent SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 26500757 26500757 C2orf39 2 C C T 29 AGBL5 60509 broad.mit.edu 36 2 27135678 27135678 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27135678 27135678 AGBL5 2 C C T 30 PSD4 23550 broad.mit.edu 36 2 113666579 113666579 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113666579 113666579 PSD4 2 C C T 19 TTN 7273 broad.mit.edu 36 2 179292396 179292396 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 179292396 179292396 TTN 2 C C T 27 LOC643905 643905 broad.mit.edu 36 2 240631022 240631022 + Silent SNP G G C novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 240631022 240631022 LOC643905 2 G G C 34 ZNF334 55713 broad.mit.edu 36 20 44563870 44563870 + Silent SNP A A G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 44563870 44563870 ZNF334 20 A A G 10 MYO18B 84700 broad.mit.edu 36 22 24573605 24573605 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24573605 24573605 MYO18B 22 G G T 40 OR5H2 79310 broad.mit.edu 36 3 99484578 99484578 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99484578 99484578 OR5H2 3 C C T 32 MYH15 22989 broad.mit.edu 36 3 109688052 109688052 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 109688052 109688052 MYH15 3 C C T 18 RNF13 11342 broad.mit.edu 36 3 151095968 151095968 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 151095968 151095968 RNF13 3 G G C 34 SI 6476 broad.mit.edu 36 3 166221865 166221865 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 166221865 166221865 SI 3 T T A 50 EVC2 132884 broad.mit.edu 36 4 5675225 5675225 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5675225 5675225 EVC2 4 G G A 34 CDS1 1040 broad.mit.edu 36 4 85774097 85774097 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 85774097 85774097 CDS1 4 C C G 32 FABP2 2169 broad.mit.edu 36 4 120460175 120460175 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 120460175 120460175 FABP2 4 A A T 16 NIPBL 25836 broad.mit.edu 36 5 37021621 37021621 + Nonsense_Mutation SNP C C A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 37021621 37021621 NIPBL 5 C C A 29 CYP39A1 51302 broad.mit.edu 36 6 46671809 46671809 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46671809 46671809 CYP39A1 6 A A T 16 PKHD1 5314 broad.mit.edu 36 6 51631990 51631990 + Silent SNP A A G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 51631990 51631990 PKHD1 6 A A G 16 FAM184A 79632 broad.mit.edu 36 6 119343135 119343135 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 119343135 119343135 FAM184A 6 G G A 40 THBS2 7058 broad.mit.edu 36 6 169390480 169390480 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 169390480 169390480 THBS2 6 C C G 23 C7orf16 10842 broad.mit.edu 36 7 31703111 31703111 + Silent SNP T T C novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 31703111 31703111 C7orf16 7 T T C 64 MAGI2 9863 broad.mit.edu 36 7 77627333 77627333 + Silent SNP G G T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 77627333 77627333 MAGI2 7 G G T 34 CALCR 799 broad.mit.edu 36 7 92946674 92946674 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 92946674 92946674 CALCR 7 G G A 40 KCNS2 3788 broad.mit.edu 36 8 99510514 99510514 + Silent SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 99510514 99510514 KCNS2 8 C C T 19 COL22A1 169044 broad.mit.edu 36 8 139884330 139884330 + Silent SNP G G A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 139884330 139884330 COL22A1 8 G G A 38 PTGDS 5730 broad.mit.edu 36 9 138994271 138994271 + Nonsense_Mutation SNP C C A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 138994271 138994271 PTGDS 9 C C A 19 MXRA5 25878 broad.mit.edu 36 X 3252751 3252751 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 3252751 3252751 MXRA5 23 C C A 28 WDR45 11152 broad.mit.edu 36 X 48820247 48820247 + Nonsense_Mutation SNP G G T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 48820247 48820247 WDR45 23 G G T 45 WNK3 65267 broad.mit.edu 36 X 54292143 54292143 + Silent SNP G G T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 54292143 54292143 WNK3 23 G G T 33 ARMCX1 51309 broad.mit.edu 36 X 100695400 100695400 + Silent SNP C C T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 100695400 100695400 ARMCX1 23 C C T 19 PAK3 5063 broad.mit.edu 36 X 110274786 110274786 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 110274786 110274786 PAK3 23 A A T 3 TP53 7157 broad.mit.edu 36 17 7518263 7518263 + Missense_Mutation SNP C C T rs11540652 byHapMap TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Missense_Mutation SNP 7518263 7518263 TP53 17 C C T 23 RB1CC1 9821 broad.mit.edu 36 8 53717636 53717638 + In_Frame_Del DEL CTT - CTT novel Unknown TCGA-13-1496-01 TCGA-13-1496-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 53717636 53717638 RB1CC1 8 CTT - CTT 20