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 DNTTIP2 30836 broad.mit.edu 36 1 94115352 94115352 + Nonsense_Mutation SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 94115352 94115352 DNTTIP2 1 G G A 48 PEAR1 375033 broad.mit.edu 36 1 155143274 155143274 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 155143274 155143274 PEAR1 1 C C T 22 FCRL1 115350 broad.mit.edu 36 1 156038814 156038814 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 156038814 156038814 FCRL1 1 C C A 22 ABL2 broad.mit.edu 36 1 177362146 177362146 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 177362146 177362146 ABL2 1 C C T 25 TOR1AIP1 26092 broad.mit.edu 36 1 178153662 178153662 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 178153662 178153662 TOR1AIP1 1 C C A 21 PGBD5 79605 broad.mit.edu 36 1 228564695 228564695 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 228564695 228564695 PGBD5 1 T T C 52 VIM 7431 broad.mit.edu 36 10 17311905 17311905 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17311905 17311905 VIM 10 C C A 25 CSGALNACT2 55454 broad.mit.edu 36 10 42982544 42982544 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 42982544 42982544 CSGALNACT2 10 C C A 25 PLA2G12B 84647 broad.mit.edu 36 10 74372423 74372423 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 74372423 74372423 PLA2G12B 10 G G A 47 C10orf12 26148 broad.mit.edu 36 10 98733844 98733844 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 98733844 98733844 C10orf12 10 G G A 48 COL17A1 1308 broad.mit.edu 36 10 105789739 105789739 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 105789739 105789739 COL17A1 10 C C A 24 TMEM132A 54972 broad.mit.edu 36 11 60457758 60457758 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60457758 60457758 TMEM132A 11 G G T 44 CD248 57124 broad.mit.edu 36 11 65839126 65839126 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 65839126 65839126 CD248 11 C C A 26 CACNA2D4 93589 broad.mit.edu 36 12 1781036 1781036 + Silent SNP G G C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 1781036 1781036 CACNA2D4 12 G G C 41 ANO6 196527 broad.mit.edu 36 12 44083507 44083507 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44083507 44083507 ANO6 12 C C T 32 NUP37 79023 broad.mit.edu 36 12 101036303 101036303 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 101036303 101036303 NUP37 12 T T C 61 PAH 5053 broad.mit.edu 36 12 101762268 101762268 + Silent SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 101762268 101762268 PAH 12 G G A 41 ACAD10 80724 broad.mit.edu 36 12 110668393 110668393 + Silent SNP A A G novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 110668393 110668393 ACAD10 12 A A G 1 RASAL1 8437 broad.mit.edu 36 12 112036991 112036991 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 112036991 112036991 RASAL1 12 G G A 44 FAM123A 219287 broad.mit.edu 36 13 24642713 24642713 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24642713 24642713 FAM123A 13 C C A 25 EVL 51466 broad.mit.edu 36 14 99664688 99664688 + Silent SNP A A C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 99664688 99664688 EVL 14 A A C 6 TP53 7157 broad.mit.edu 36 17 7520099 7520099 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7520099 7520099 TP53 17 C C A 22 RNF43 54894 broad.mit.edu 36 17 53795899 53795899 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53795899 53795899 RNF43 17 G G C 34 CYP2A7 1549 broad.mit.edu 36 19 46076681 46076681 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 46076681 46076681 CYP2A7 19 G G T 34 PTOV1 53635 broad.mit.edu 36 19 55049528 55049528 + Silent SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 55049528 55049528 PTOV1 19 G G A 42 EPS8L1 54869 broad.mit.edu 36 19 60289342 60289342 + Silent SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 60289342 60289342 EPS8L1 19 G G A 46 WDR35 57539 broad.mit.edu 36 2 19977517 19977517 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19977517 19977517 WDR35 2 G G C 33 MPHOSPH10 10199 broad.mit.edu 36 2 71211344 71211344 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71211344 71211344 MPHOSPH10 2 G G C 48 TRAK2 66008 broad.mit.edu 36 2 201953923 201953923 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 201953923 201953923 TRAK2 2 G G A 47 BMPR2 659 broad.mit.edu 36 2 203129284 203129284 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 203129284 203129284 BMPR2 2 T T C 55 COL6A3 1293 broad.mit.edu 36 2 237940387 237940387 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 237940387 237940387 COL6A3 2 C C A 18 BCL2L13 23786 broad.mit.edu 36 22 16589790 16589790 + Silent SNP C C T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 16589790 16589790 BCL2L13 22 C C T 23 SULT4A1 25830 broad.mit.edu 36 22 42589571 42589572 + Missense_Mutation DNP GG GG CT novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 42589571 42589572 SULT4A1 22 GG GG CT 43 TTLL8 164714 broad.mit.edu 36 22 48825840 48825840 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 48825840 48825840 TTLL8 22 G G T 42 ATP2B2 491 broad.mit.edu 36 3 10392222 10392222 + Silent SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 10392222 10392222 ATP2B2 3 G G A 40 GOLGB1 2804 broad.mit.edu 36 3 122899551 122899551 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 122899551 122899551 GOLGB1 3 G G C 35 IGSF10 285313 broad.mit.edu 36 3 152644252 152644252 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 152644252 152644252 IGSF10 3 C C T 27 MSX1 4487 broad.mit.edu 36 4 4915395 4915395 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 4915395 4915395 MSX1 4 T T G 62 KLKB1 3818 broad.mit.edu 36 4 187390383 187390383 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 187390383 187390383 KLKB1 4 G G A 35 SLC6A3 6531 broad.mit.edu 36 5 1485744 1485744 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1485744 1485744 SLC6A3 5 G G A 38 IL13 3596 broad.mit.edu 36 5 132021782 132021782 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 132021782 132021782 IL13 5 A A G 8 ITK 3702 broad.mit.edu 36 5 156605577 156605577 + Silent SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 156605577 156605577 ITK 5 G G A 48 CDHR2 54825 broad.mit.edu 36 5 175945614 175945614 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 175945614 175945614 CDHR2 5 C C T 26 EXOC2 55770 broad.mit.edu 36 6 498866 498866 + Silent SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 498866 498866 EXOC2 6 G G A 45 WRNIP1 56897 broad.mit.edu 36 6 2730292 2730292 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 2730292 2730292 WRNIP1 6 A A T 11 MICAL1 64780 broad.mit.edu 36 6 109875077 109875077 + Silent SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 109875077 109875077 MICAL1 6 G G A 35 CHMP7 91782 broad.mit.edu 36 8 23174003 23174003 + Silent SNP C C T novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 23174003 23174003 CHMP7 8 C C T 30 LRP12 29967 broad.mit.edu 36 8 105590452 105590452 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 105590452 105590452 LRP12 8 G G C 40 EXT1 2131 broad.mit.edu 36 8 118899870 118899870 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 A C A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 118899870 118899870 EXT1 8 A A C 5 IKBKAP 8518 broad.mit.edu 36 9 110691487 110691487 + Silent SNP C C G novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 110691487 110691487 IKBKAP 9 C C G 21 CCDC120 90060 broad.mit.edu 36 X 48812186 48812186 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 48812186 48812186 CCDC120 23 G G A 34 STARD8 9754 broad.mit.edu 36 X 67854095 67854095 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 67854095 67854095 STARD8 23 G G A 40 LPAR4 2846 broad.mit.edu 36 X 77897514 77897514 + Silent SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 77897514 77897514 LPAR4 23 C C A 30 DCAF12L1 139170 broad.mit.edu 36 X 125512955 125512955 + Nonsense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Nonsense_Mutation SNP 125512955 125512955 DCAF12L1 23 C C A 29 BCORL1 63035 broad.mit.edu 36 X 128990344 128990344 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128990344 128990344 BCORL1 23 C C A 24 NBPF10 100132406 broad.mit.edu 36 1 144038903 144038907 + Frame_Shift_Del DEL TGAAT - TGAAT novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 144038903 144038907 NBPF10 1 TGAAT - TGAAT 55 SUSD4 55061 broad.mit.edu 36 1 221603325 221603326 + In_Frame_Ins INS - TGC - novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Ins INS 221603325 221603326 SUSD4 1 - TGC - 60 RCOR2 283248 broad.mit.edu 36 11 63438490 63438510 + In_Frame_Del DEL CCAGCCGCCGGGCCTGTCTGT - CCAGCCGCCGGGCCTGTCTGT novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 63438490 63438510 RCOR2 11 CCAGCCGCCGGGCCTGTCTGT - CCAGCCGCCGGGCCTGTCTGT 22 TGIF1 7050 broad.mit.edu 36 18 3442223 3442223 + Frame_Shift_Del DEL T - T rs11571510 byCluster TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 3442223 3442223 TGIF1 18 T - T 54 FAM86B2 653333 broad.mit.edu 36 8 12335964 12335966 + In_Frame_Del DEL CTG - CTG novel Unknown TCGA-13-1494-01 TCGA-13-1494-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 12335964 12335966 FAM86B2 8 CTG - CTG 32