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 SLC6A9 6536 broad.mit.edu 36 1 44235940 44235940 + Missense_Mutation SNP C C T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44235940 44235940 SLC6A9 1 C C T 23 SGIP1 84251 broad.mit.edu 36 1 66978959 66978959 + Silent SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 66978959 66978959 SGIP1 1 G G A 33 STXBP3 6814 broad.mit.edu 36 1 109102718 109102718 + Missense_Mutation SNP A A G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 109102718 109102718 STXBP3 1 A A G 16 SELP 6403 broad.mit.edu 36 1 167832958 167832958 + Missense_Mutation SNP A A T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 167832958 167832958 SELP 1 A A T 11 RYR2 6262 broad.mit.edu 36 1 235878517 235878517 + Missense_Mutation SNP C C T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 235878517 235878517 RYR2 1 C C T 27 KIAA1217 56243 broad.mit.edu 36 10 24850793 24850793 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24850793 24850793 KIAA1217 10 G G T 35 SGMS1 259230 broad.mit.edu 36 10 51741170 51741170 + Silent SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 51741170 51741170 SGMS1 10 G G A 36 DPYSL4 10570 broad.mit.edu 36 10 133858397 133858398 + Missense_Mutation DNP GG GG AA novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 133858397 133858398 DPYSL4 10 GG GG AA 43 NLRP10 338322 broad.mit.edu 36 11 7941372 7941372 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7941372 7941372 NLRP10 11 G G T 35 RSF1 51773 broad.mit.edu 36 11 77129624 77129624 + Silent SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 77129624 77129624 RSF1 11 G G A 33 EXPH5 23086 broad.mit.edu 36 11 107890584 107890584 + Missense_Mutation SNP A A G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 107890584 107890584 EXPH5 11 A A G 1 KCNA1 3736 broad.mit.edu 36 12 4890821 4890821 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 4890821 4890821 KCNA1 12 G G C 47 GPR162 27239 broad.mit.edu 36 12 6806506 6806506 + Missense_Mutation SNP T T C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6806506 6806506 GPR162 12 T T C 60 FOXJ2 55810 broad.mit.edu 36 12 8091930 8091930 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 8091930 8091930 FOXJ2 12 C C G 30 KRT73 319101 broad.mit.edu 36 12 51298331 51298331 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51298331 51298331 KRT73 12 G G A 34 ZNF605 100289635 broad.mit.edu 36 12 132019805 132019805 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 132019805 132019805 ZNF605 12 C C G 29 LPAR6 10161 broad.mit.edu 36 13 47884114 47884114 + Silent SNP T T G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 47884114 47884114 LPAR6 13 T T G 59 DAAM1 23002 broad.mit.edu 36 14 58891744 58891744 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 58891744 58891744 DAAM1 14 C C G 25 SPRED1 161742 broad.mit.edu 36 15 36430560 36430560 + Silent SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 36430560 36430560 SPRED1 15 C C G 29 DISP2 85455 broad.mit.edu 36 15 38449614 38449614 + Missense_Mutation SNP C C T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38449614 38449614 DISP2 15 C C T 27 FOXB1 27023 broad.mit.edu 36 15 58084726 58084726 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 58084726 58084726 FOXB1 15 C C G 21 SV2B 9899 broad.mit.edu 36 15 89602662 89602662 + Silent SNP C C T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 89602662 89602662 SV2B 15 C C T 28 GSG1L 146395 broad.mit.edu 36 16 27747764 27747764 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27747764 27747764 GSG1L 16 G G A 41 ZC3H18 124245 broad.mit.edu 36 16 87193846 87193846 + Silent SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 87193846 87193846 ZC3H18 16 C C G 29 TP53 7157 broad.mit.edu 36 17 7518993 7518993 + Missense_Mutation SNP A A C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7518993 7518993 TP53 17 A A C 3 LIG3 3980 broad.mit.edu 36 17 30337216 30337216 + Missense_Mutation SNP C C T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30337216 30337216 LIG3 17 C C T 26 MYL4 4635 broad.mit.edu 36 17 42654065 42654065 + Missense_Mutation SNP T T C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42654065 42654065 MYL4 17 T T C 55 LAMA1 284217 broad.mit.edu 36 18 6982560 6982560 + Missense_Mutation SNP T T G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6982560 6982560 LAMA1 18 T T G 56 ZNF236 7776 broad.mit.edu 36 18 72766420 72766420 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 72766420 72766420 ZNF236 18 G G A 48 GNA11 2767 broad.mit.edu 36 19 3070021 3070021 + Nonsense_Mutation SNP C C A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 3070021 3070021 GNA11 19 C C A 19 MLL4 9757 broad.mit.edu 36 19 40910339 40910339 + Silent SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 40910339 40910339 MLL4 19 G G A 47 CEACAM8 1088 broad.mit.edu 36 19 47785548 47785548 + Silent SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 47785548 47785548 CEACAM8 19 G G A 33 LTBP1 4052 broad.mit.edu 36 2 33444027 33444027 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33444027 33444027 LTBP1 2 G G A 41 SLC20A1 6574 broad.mit.edu 36 2 113131287 113131287 + Missense_Mutation SNP A A T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113131287 113131287 SLC20A1 2 A A T 9 PROC 5624 broad.mit.edu 36 2 127893996 127893996 + Missense_Mutation SNP A A C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 127893996 127893996 PROC 2 A A C 7 OLA1 29789 broad.mit.edu 36 2 174714837 174714837 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 174714837 174714837 OLA1 2 C C G 26 ANKRD44 91526 broad.mit.edu 36 2 197586552 197586552 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 197586552 197586552 ANKRD44 2 C C G 28 SP140 11262 broad.mit.edu 36 2 230883744 230883744 + Silent SNP G G C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 230883744 230883744 SP140 2 G G C 39 C20orf117 140710 broad.mit.edu 36 20 34877606 34877606 + Silent SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 34877606 34877606 C20orf117 20 G G A 40 ZBTB46 140685 broad.mit.edu 36 20 61891960 61891960 + Nonsense_Mutation SNP C C A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 61891960 61891960 ZBTB46 20 C C A 32 MX2 4600 broad.mit.edu 36 21 41676280 41676280 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 41676280 41676280 MX2 21 G G T 35 ZC3H7B 23264 broad.mit.edu 36 22 40056026 40056026 + Silent SNP A A T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 40056026 40056026 ZC3H7B 22 A A T 11 EFHB 151651 broad.mit.edu 36 3 19896296 19896296 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19896296 19896296 EFHB 3 G G A 46 C3orf35 339883 broad.mit.edu 36 3 37451453 37451453 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37451453 37451453 C3orf35 3 G G T 41 FAM116A 201627 broad.mit.edu 36 3 57622228 57622228 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 57622228 57622228 FAM116A 3 G G C 44 CLDN18 51208 broad.mit.edu 36 3 139200538 139200538 + Nonsense_Mutation SNP C C A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 139200538 139200538 CLDN18 3 C C A 18 TLR6 10333 broad.mit.edu 36 4 38506153 38506153 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38506153 38506153 TLR6 4 C C G 32 FGA 2243 broad.mit.edu 36 4 155726337 155726337 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 155726337 155726337 FGA 4 G G T 35 PAIP1 10605 broad.mit.edu 36 5 43574851 43574851 + Missense_Mutation SNP C C A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43574851 43574851 PAIP1 5 C C A 30 ITGA1 3672 broad.mit.edu 36 5 52219427 52219427 + Missense_Mutation SNP G G A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52219427 52219427 ITGA1 5 G G A 39 SKIV2L2 23517 broad.mit.edu 36 5 54729004 54729004 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54729004 54729004 SKIV2L2 5 G G C 48 IL3 3562 broad.mit.edu 36 5 131426278 131426278 + Silent SNP C C A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 131426278 131426278 IL3 5 C C A 29 PCDHB14 56122 broad.mit.edu 36 5 140583647 140583647 + Missense_Mutation SNP A A T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140583647 140583647 PCDHB14 5 A A T 6 ANKS1A 23294 broad.mit.edu 36 6 35058566 35058566 + Missense_Mutation SNP A A C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35058566 35058566 ANKS1A 6 A A C 1 KLC4 89953 broad.mit.edu 36 6 43147302 43147302 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43147302 43147302 KLC4 6 G G C 41 TNRC18B 84629 broad.mit.edu 36 7 5368104 5368104 + Nonsense_Mutation SNP G G C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 5368104 5368104 TNRC18B 7 G G C 48 SP4 6671 broad.mit.edu 36 7 21436551 21436551 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 21436551 21436551 SP4 7 C C G 17 HOXA1 3198 broad.mit.edu 36 7 27101659 27101659 + Missense_Mutation SNP C C T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27101659 27101659 HOXA1 7 C C T 30 NEUROD6 63974 broad.mit.edu 36 7 31344732 31344732 + Missense_Mutation SNP C C G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31344732 31344732 NEUROD6 7 C C G 29 BCL7B 9275 broad.mit.edu 36 7 72604447 72604447 + Missense_Mutation SNP T T A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 72604447 72604447 BCL7B 7 T T A 58 KIAA1324L 222223 broad.mit.edu 36 7 86382045 86382045 + Missense_Mutation SNP G G T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 86382045 86382045 KIAA1324L 7 G G T 44 CROT 54677 broad.mit.edu 36 7 86865895 86865895 + Nonstop_Mutation SNP A A G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Nonstop_Mutation SNP 86865895 86865895 CROT 7 A A G 15 ZNF804B 219578 broad.mit.edu 36 7 88803028 88803028 + Silent SNP A A G novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 88803028 88803028 ZNF804B 7 A A G 14 DLX5 1749 broad.mit.edu 36 7 96491753 96491753 + Missense_Mutation SNP G G C novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 96491753 96491753 DLX5 7 G G C 33 ABCA1 19 broad.mit.edu 36 9 106639096 106639096 + Missense_Mutation SNP T T A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 106639096 106639096 ABCA1 9 T T A 52 USP20 10868 broad.mit.edu 36 9 131671877 131671877 + Missense_Mutation SNP C C T novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 131671877 131671877 USP20 9 C C T 26 ANAPC2 29882 broad.mit.edu 36 9 139194469 139194469 + Missense_Mutation SNP C C A novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 139194469 139194469 ANAPC2 9 C C A 20 ADAMTS18 170692 broad.mit.edu 36 16 75958960 75958971 + In_Frame_Del DEL GCCGGGGTAGCC - GCCGGGGTAGCC novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 75958960 75958971 ADAMTS18 16 GCCGGGGTAGCC - GCCGGGGTAGCC 34 FAM86B2 653333 broad.mit.edu 36 8 12335964 12335966 + In_Frame_Del DEL CTG - CTG novel Unknown TCGA-25-2401-01 TCGA-25-2401-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 12335964 12335966 FAM86B2 8 CTG - CTG 32