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 ZC3H12A 80149 broad.mit.edu 36 1 37718539 37718539 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37718539 37718539 ZC3H12A 1 G G A 41 SNX7 51375 broad.mit.edu 36 1 98929307 98929307 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 98929307 98929307 SNX7 1 C C G 25 CELSR2 1952 broad.mit.edu 36 1 109595278 109595278 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 109595278 109595278 CELSR2 1 C C T 23 CD1D 912 broad.mit.edu 36 1 156419305 156419305 + Silent SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 156419305 156419305 CD1D 1 C C T 24 CACNA1E 777 broad.mit.edu 36 1 179992811 179992811 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179992811 179992811 CACNA1E 1 G G C 48 PFKFB3 5209 broad.mit.edu 36 10 6301558 6301558 + Silent SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 6301558 6301558 PFKFB3 10 G G A 39 ATAD1 84896 broad.mit.edu 36 10 89504434 89504434 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89504434 89504434 ATAD1 10 C C A 17 TRAF6 7189 broad.mit.edu 36 11 36468137 36468137 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36468137 36468137 TRAF6 11 G G A 40 CNTN5 53942 broad.mit.edu 36 11 99220797 99220797 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99220797 99220797 CNTN5 11 G G A 36 C11orf87 399947 broad.mit.edu 36 11 108800039 108800039 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 108800039 108800039 C11orf87 11 C C G 23 STYK1 55359 broad.mit.edu 36 12 10666533 10666533 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10666533 10666533 STYK1 12 C C A 22 CASC1 55259 broad.mit.edu 36 12 25188760 25188760 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 25188760 25188760 CASC1 12 G G A 46 TMEM132D 121256 broad.mit.edu 36 12 128132269 128132269 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128132269 128132269 TMEM132D 12 C C T 29 RPGRIP1 57096 broad.mit.edu 36 14 20855751 20855751 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20855751 20855751 RPGRIP1 14 C C A 27 DACT1 51339 broad.mit.edu 36 14 58182236 58182236 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 58182236 58182236 DACT1 14 C C T 23 AHNAK2 113146 broad.mit.edu 36 14 104483452 104483452 + Silent SNP C C A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 104483452 104483452 AHNAK2 14 C C A 22 THBS1 7057 broad.mit.edu 36 15 37668063 37668063 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37668063 37668063 THBS1 15 G G C 48 RPLP1 6176 broad.mit.edu 36 15 67532363 67532363 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 67532363 67532363 RPLP1 15 G G A 38 MYH8 4626 broad.mit.edu 36 17 10243635 10243635 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10243635 10243635 MYH8 17 C C T 23 TRIM16 10626 broad.mit.edu 36 17 15475745 15475745 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 15475745 15475745 TRIM16 17 C C A 29 NSF 4905 broad.mit.edu 36 17 42184080 42184080 + Silent SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 42184080 42184080 NSF 17 G G A 34 THOC1 9984 broad.mit.edu 36 18 213447 213447 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 213447 213447 THOC1 18 C C G 32 DSG4 147409 broad.mit.edu 36 18 27222370 27222370 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27222370 27222370 DSG4 18 A A T 12 TSHZ3 57616 broad.mit.edu 36 19 36460292 36460292 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 36460292 36460292 TSHZ3 19 C C T 25 ZNF274 10782 broad.mit.edu 36 19 63416303 63416303 + Silent SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 63416303 63416303 ZNF274 19 G G A 33 GMCL1 64395 broad.mit.edu 36 2 69930290 69930290 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 69930290 69930290 GMCL1 2 G G T 41 C2orf65 130951 broad.mit.edu 36 2 74640855 74640855 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74640855 74640855 C2orf65 2 G G T 44 SEMA4F 10505 broad.mit.edu 36 2 74743412 74743412 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74743412 74743412 SEMA4F 2 G G A 43 STAM2 10254 broad.mit.edu 36 2 152696898 152696898 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 152696898 152696898 STAM2 2 T T G 50 ZNF804A 91752 broad.mit.edu 36 2 185508769 185508769 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 185508769 185508769 ZNF804A 2 G G A 42 PNKD 25953 broad.mit.edu 36 2 218916522 218916522 + Silent SNP G G T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 218916522 218916522 PNKD 2 G G T 47 PASK 23178 broad.mit.edu 36 2 241726813 241726813 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 241726813 241726813 PASK 2 G G A 38 C20orf26 26074 broad.mit.edu 36 20 20180314 20180314 + Silent SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 20180314 20180314 C20orf26 20 C C T 23 GTSE1 51512 broad.mit.edu 36 22 45088481 45088481 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45088481 45088481 GTSE1 22 C C T 18 CSRNP1 64651 broad.mit.edu 36 3 39160039 39160039 + Silent SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 39160039 39160039 CSRNP1 3 G G A 48 RAD54L2 23132 broad.mit.edu 36 3 51638464 51638464 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51638464 51638464 RAD54L2 3 G G A 38 PHLDB2 90102 broad.mit.edu 36 3 113086296 113086296 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113086296 113086296 PHLDB2 3 G G A 41 PHLDB2 90102 broad.mit.edu 36 3 113176058 113176058 + Silent SNP T T C novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 113176058 113176058 PHLDB2 3 T T C 61 ACAD11 84129 broad.mit.edu 36 3 133861225 133861225 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 133861225 133861225 ACAD11 3 C C T 31 SLITRK3 22865 broad.mit.edu 36 3 166389115 166389115 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 166389115 166389115 SLITRK3 3 G G T 42 PEX5L 51555 broad.mit.edu 36 3 181010040 181010040 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 181010040 181010040 PEX5L 3 T T G 56 UBXN7 26043 broad.mit.edu 36 3 197603086 197603086 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 197603086 197603086 UBXN7 3 C C G 29 ADAMTS19 171019 broad.mit.edu 36 5 128825299 128825299 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128825299 128825299 ADAMTS19 5 C C A 28 HAVCR1 26762 broad.mit.edu 36 5 156415058 156415058 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 156415058 156415058 HAVCR1 5 G G C 36 ASCC3 10973 broad.mit.edu 36 6 101064638 101064638 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 101064638 101064638 ASCC3 6 T T C 50 UST 10090 broad.mit.edu 36 6 149327285 149327285 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 149327285 149327285 UST 6 G G A 40 PDE10A 10846 broad.mit.edu 36 6 165726274 165726274 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 165726274 165726274 PDE10A 6 A A C 3 PSMB1 5689 broad.mit.edu 36 6 170688290 170688290 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 170688290 170688290 PSMB1 6 C C G 30 DNAH11 8701 broad.mit.edu 36 7 21693297 21693297 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21693297 21693297 DNAH11 7 G G T 47 FZD1 8321 broad.mit.edu 36 7 90732932 90732932 + Silent SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 90732932 90732932 FZD1 7 C C T 27 FOXP2 93986 broad.mit.edu 36 7 114089391 114089391 + Nonsense_Mutation SNP T T A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 114089391 114089391 FOXP2 7 T T A 60 OR6B1 135946 broad.mit.edu 36 7 143332853 143332853 + Silent SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 143332853 143332853 OR6B1 7 C C T 21 CNTNAP2 26047 broad.mit.edu 36 7 147545369 147545369 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 147545369 147545369 CNTNAP2 7 G G A 34 PRKDC 5591 broad.mit.edu 36 8 49004231 49004231 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 49004231 49004231 PRKDC 8 C C T 25 ZNF706 51123 broad.mit.edu 36 8 102283138 102283138 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 102283138 102283138 ZNF706 8 C C G 19 RIMS2 9699 broad.mit.edu 36 8 105042518 105042518 + Silent SNP T T C novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 105042518 105042518 RIMS2 8 T T C 51 PKHD1L1 93035 broad.mit.edu 36 8 110526851 110526851 + Silent SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 110526851 110526851 PKHD1L1 8 C C T 25 KIAA0196 9897 broad.mit.edu 36 8 126160301 126160301 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 126160301 126160301 KIAA0196 8 C C A 31 KIAA2026 158358 broad.mit.edu 36 9 5913129 5913129 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 5913129 5913129 KIAA2026 9 C C T 28 ZNF462 58499 broad.mit.edu 36 9 108727368 108727368 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 108727368 108727368 ZNF462 9 C C T 19 MAGEB16 139604 broad.mit.edu 36 X 35730701 35730701 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35730701 35730701 MAGEB16 23 T T G 55 IL1RAPL2 26280 broad.mit.edu 36 X 104327040 104327040 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 104327040 104327040 IL1RAPL2 23 C C A 29 ZBTB33 10009 broad.mit.edu 36 X 119272073 119272073 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 119272073 119272073 ZBTB33 23 A A G 11 TP53 7157 broad.mit.edu 36 17 7519266 7519267 + Frame_Shift_Ins INS - - GG novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 7519266 7519267 TP53 17 - - GG 11 LPAR3 23566 broad.mit.edu 36 1 85103869 85103869 + Frame_Shift_Del DEL C - C novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 85103869 85103869 LPAR3 1 C - C 25 CT47B1 643311 broad.mit.edu 36 X 119892825 119892851 + In_Frame_Del DEL TCCTCTGTGGCCTCCTCTGTGAGCTTC - TCCTCTGTGGCCTCCTCTGTGAGCTTC novel Unknown TCGA-13-1410-01 TCGA-13-1410-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 119892825 119892851 CT47B1 23 TCCTCTGTGGCCTCCTCTGTGAGCTTC - TCCTCTGTGGCCTCCTCTGTGAGCTTC 62