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 BAI2 576 broad.mit.edu 36 1 31994493 31994493 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31994493 31994493 BAI2 1 G G T 35 KHDRBS1 10657 broad.mit.edu 36 1 32276782 32276782 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 32276782 32276782 KHDRBS1 1 G G A 37 ERMAP 114625 broad.mit.edu 36 1 43080955 43080955 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43080955 43080955 ERMAP 1 A A T 16 EIF2B3 8891 broad.mit.edu 36 1 45113910 45113910 + Silent SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 45113910 45113910 EIF2B3 1 G G C 41 POMGNT1 55624 broad.mit.edu 36 1 46431602 46431602 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 46431602 46431602 POMGNT1 1 G G C 46 USP24 23358 broad.mit.edu 36 1 55363661 55363661 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55363661 55363661 USP24 1 A A T 12 SF3B4 10262 broad.mit.edu 36 1 148164355 148164355 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 148164355 148164355 SF3B4 1 G G A 41 ARHGEF11 9826 broad.mit.edu 36 1 155177816 155177816 + Silent SNP A A T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 155177816 155177816 ARHGEF11 1 A A T 6 FAM20B 9917 broad.mit.edu 36 1 177279714 177279714 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 177279714 177279714 FAM20B 1 G G A 41 KLHDC8A 55220 broad.mit.edu 36 1 203579005 203579005 + Silent SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 203579005 203579005 KLHDC8A 1 G G C 47 USH2A 7399 broad.mit.edu 36 1 214447291 214447291 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 214447291 214447291 USH2A 1 C C T 20 VWA2 340706 broad.mit.edu 36 10 116027764 116027764 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 116027764 116027764 VWA2 10 G G T 34 MTG1 92170 broad.mit.edu 36 10 135082980 135082980 + Silent SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 135082980 135082980 MTG1 10 G G C 46 ART5 116969 broad.mit.edu 36 11 3617997 3617997 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 3617997 3617997 ART5 11 G G A 37 ACCSL 390110 broad.mit.edu 36 11 44034203 44034203 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44034203 44034203 ACCSL 11 A A T 14 ATM 472 broad.mit.edu 36 11 107741029 107741029 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 107741029 107741029 ATM 11 A A G 16 DIXDC1 85458 broad.mit.edu 36 11 111361233 111361233 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 111361233 111361233 DIXDC1 11 G G A 44 MCAM 4162 broad.mit.edu 36 11 118687796 118687796 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 118687796 118687796 MCAM 11 C C G 27 CD163L1 283316 broad.mit.edu 36 12 7477313 7477313 + Silent SNP A A G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 7477313 7477313 CD163L1 12 A A G 11 PDE3A 5139 broad.mit.edu 36 12 20691141 20691141 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20691141 20691141 PDE3A 12 G G C 36 KRT6A 3853 broad.mit.edu 36 12 51167847 51167847 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51167847 51167847 KRT6A 12 C C A 28 MTUS2 23281 broad.mit.edu 36 13 28497077 28497077 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28497077 28497077 MTUS2 13 T T C 56 MAB21L1 4081 broad.mit.edu 36 13 34947751 34947751 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 34947751 34947751 MAB21L1 13 T T G 52 NDFIP2 54602 broad.mit.edu 36 13 78993083 78993083 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 T A T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 78993083 78993083 NDFIP2 13 T T A 57 OR6S1 341799 broad.mit.edu 36 14 20179490 20179490 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20179490 20179490 OR6S1 14 G G C 44 MDGA2 161357 broad.mit.edu 36 14 46458974 46458974 + Silent SNP G G T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 46458974 46458974 MDGA2 14 G G T 46 ZC3H14 79882 broad.mit.edu 36 14 88109076 88109076 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 88109076 88109076 ZC3H14 14 G G C 33 HCN4 10021 broad.mit.edu 36 15 71422832 71422832 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71422832 71422832 HCN4 15 A A T 3 UBE2Q2 92912 broad.mit.edu 36 15 73952823 73952823 + Splice_Site_SNP SNP G G T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 73952823 73952823 UBE2Q2 15 G G T 35 ITFG1 81533 broad.mit.edu 36 16 46052298 46052298 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46052298 46052298 ITFG1 16 C C A 23 TP53 7157 broad.mit.edu 36 17 7519221 7519221 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7519221 7519221 TP53 17 A A T 7 PER1 5187 broad.mit.edu 36 17 7992067 7992067 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7992067 7992067 PER1 17 G G C 44 ACLY 47 broad.mit.edu 36 17 37278556 37278556 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37278556 37278556 ACLY 17 G G C 34 NOTUM 147111 broad.mit.edu 36 17 77504235 77504235 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77504235 77504235 NOTUM 17 C C A 29 ANKRD29 147463 broad.mit.edu 36 18 19472839 19472839 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19472839 19472839 ANKRD29 18 A A C 1 ZNF57 126295 broad.mit.edu 36 19 2868849 2868849 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2868849 2868849 ZNF57 19 T T G 52 OR7D4 125958 broad.mit.edu 36 19 9185997 9185997 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 9185997 9185997 OR7D4 19 C C T 29 SMARCA4 6597 broad.mit.edu 36 19 10966512 10966512 + Silent SNP C C A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 10966512 10966512 SMARCA4 19 C C A 29 MLL4 9757 broad.mit.edu 36 19 40904188 40904188 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40904188 40904188 MLL4 19 A A G 2 ATP1A3 478 broad.mit.edu 36 19 47164836 47164836 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47164836 47164836 ATP1A3 19 C C A 20 CACNG6 59285 broad.mit.edu 36 19 59207216 59207216 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 59207216 59207216 CACNG6 19 G G A 43 HEATR5B 54497 broad.mit.edu 36 2 37108713 37108713 + Nonsense_Mutation SNP G G T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 37108713 37108713 HEATR5B 2 G G T 45 FAM161A 84140 broad.mit.edu 36 2 61920764 61920764 + Silent SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 61920764 61920764 FAM161A 2 G G C 41 FER1L5 90342 broad.mit.edu 36 2 96727007 96727007 + Silent SNP C C T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 96727007 96727007 FER1L5 2 C C T 17 CCNT2 905 broad.mit.edu 36 2 135428333 135428333 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 135428333 135428333 CCNT2 2 G G A 34 DPP4 1803 broad.mit.edu 36 2 162589667 162589667 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 162589667 162589667 DPP4 2 C C T 26 ABCA12 26154 broad.mit.edu 36 2 215551883 215551883 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 215551883 215551883 ABCA12 2 A A G 4 MARCH4 57574 broad.mit.edu 36 2 216850783 216850783 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 216850783 216850783 MARCH4 2 G G C 42 FAM134A 79137 broad.mit.edu 36 2 219753079 219753079 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 219753079 219753079 FAM134A 2 G G C 35 PCSK2 5126 broad.mit.edu 36 20 17394023 17394023 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17394023 17394023 PCSK2 20 C C T 19 STAU1 6780 broad.mit.edu 36 20 47174417 47174417 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47174417 47174417 STAU1 20 C C T 27 GCNT4 51301 broad.mit.edu 36 5 74360422 74360422 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74360422 74360422 GCNT4 5 C C A 18 FBXO38 81545 broad.mit.edu 36 5 147775749 147775749 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 147775749 147775749 FBXO38 5 T T A 54 RUFY1 80230 broad.mit.edu 36 5 178945450 178945450 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 178945450 178945450 RUFY1 5 C C G 20 HIST1H1A 3024 broad.mit.edu 36 6 26125656 26125656 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 26125656 26125656 HIST1H1A 6 G G C 40 ZNF184 7738 broad.mit.edu 36 6 27527992 27527992 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27527992 27527992 ZNF184 6 C C G 22 GNL1 2794 broad.mit.edu 36 6 30629215 30629215 + Silent SNP A A G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 30629215 30629215 GNL1 6 A A G 11 SYTL3 94120 broad.mit.edu 36 6 159006487 159006487 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 159006487 159006487 SYTL3 6 G G C 36 DAGLB 221955 broad.mit.edu 36 7 6442674 6442674 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 6442674 6442674 DAGLB 7 G G A 35 EGFR 1956 broad.mit.edu 36 7 55240662 55240662 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 55240662 55240662 EGFR 7 A A G 5 CPA4 51200 broad.mit.edu 36 7 129737955 129737955 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 129737955 129737955 CPA4 7 C C A 21 AKR1B10L 441282 broad.mit.edu 36 7 133910733 133910733 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 133910733 133910733 AKR1B10L 7 G G A 37 ZNF746 155061 broad.mit.edu 36 7 148822461 148822461 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 148822461 148822461 ZNF746 7 G G A 37 GPR124 25960 broad.mit.edu 36 8 37809764 37809764 + Silent SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 37809764 37809764 GPR124 8 G G C 43 HRSP12 10247 broad.mit.edu 36 8 99185949 99185949 + Splice_Site_SNP SNP C C G novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 99185949 99185949 HRSP12 8 C C G 32 POP1 10940 broad.mit.edu 36 8 99239036 99239036 + Silent SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 99239036 99239036 POP1 8 G G A 45 FLJ43860 389690 broad.mit.edu 36 8 142514506 142514506 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 142514506 142514506 FLJ43860 8 C C T 17 AK3 50808 broad.mit.edu 36 9 4708447 4708447 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 4708447 4708447 AK3 9 G G C 47 PPP1R3F 89801 broad.mit.edu 36 X 49029240 49029240 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 49029240 49029240 PPP1R3F 23 G G C 44 CCNB3 85417 broad.mit.edu 36 X 50054721 50054721 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 50054721 50054721 CCNB3 23 G G A 39 MORC4 79710 broad.mit.edu 36 X 106091944 106091944 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 106091944 106091944 MORC4 23 T T A 60 MID2 11043 broad.mit.edu 36 X 106970864 106970864 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 106970864 106970864 MID2 23 C C T 31 COL4A6 1288 broad.mit.edu 36 X 107440712 107440712 + Silent SNP T T A novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 107440712 107440712 COL4A6 23 T T A 54 GLDC 2731 broad.mit.edu 36 9 6544727 6544736 + Frame_Shift_Del DEL GAAGATTTAG - GAAGATTTAG novel Unknown TCGA-13-1501-01 TCGA-13-1501-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 6544727 6544736 GLDC 9 GAAGATTTAG - GAAGATTTAG 45