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 ZNF644 84146 broad.mit.edu 36 1 91178903 91178904 + Missense_Mutation DNP GA GA TT novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 91178903 91178904 ZNF644 1 GA GA TT 45 HMCN1 83872 broad.mit.edu 36 1 184326562 184326562 + Silent SNP T T C novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 184326562 184326562 HMCN1 1 T T C 62 TP53BP2 7159 broad.mit.edu 36 1 222052709 222052709 + Silent SNP G G A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 222052709 222052709 TP53BP2 1 G G A 43 VN1R5 317705 broad.mit.edu 36 1 245486694 245486694 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 245486694 245486694 VN1R5 1 C C T 24 NUDT5 11164 broad.mit.edu 36 10 12252907 12252907 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 12252907 12252907 NUDT5 10 C C A 30 RUFY2 55680 broad.mit.edu 36 10 69775776 69775776 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 69775776 69775776 RUFY2 10 C C G 32 LRRC55 219527 broad.mit.edu 36 11 56706465 56706465 + Silent SNP C C T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 56706465 56706465 LRRC55 11 C C T 17 FOSL1 8061 broad.mit.edu 36 11 65421052 65421052 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 65421052 65421052 FOSL1 11 T T C 56 SSH3 54961 broad.mit.edu 36 11 66831958 66831958 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 66831958 66831958 SSH3 11 G G T 36 CNTN1 1272 broad.mit.edu 36 12 39623793 39623793 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39623793 39623793 CNTN1 12 G G C 35 SILV 6490 broad.mit.edu 36 12 54646039 54646039 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 54646039 54646039 SILV 12 G G C 42 PEBP1 5037 broad.mit.edu 36 12 117060263 117060263 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 117060263 117060263 PEBP1 12 C C G 32 ATP12A 479 broad.mit.edu 36 13 24162510 24162510 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24162510 24162510 ATP12A 13 C C A 18 DDHD1 80821 broad.mit.edu 36 14 52640269 52640269 + Silent SNP C C T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 52640269 52640269 DDHD1 14 C C T 28 KIAA1409 57578 broad.mit.edu 36 14 93148948 93148948 + Silent SNP C C T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 93148948 93148948 KIAA1409 14 C C T 19 FES 2242 broad.mit.edu 36 15 89229808 89229808 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 89229808 89229808 FES 15 G G C 41 TP53 7157 broad.mit.edu 36 17 7519131 7519131 + Missense_Mutation SNP C C T rs28934578 Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7519131 7519131 TP53 17 C C T 27 IKZF3 22806 broad.mit.edu 36 17 35175946 35175946 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 35175946 35175946 IKZF3 17 C C G 31 FADS6 283985 broad.mit.edu 36 17 70386174 70386175 + Missense_Mutation DNP GT GT CG novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 70386174 70386175 FADS6 17 GT GT CG 40 TYK2 7297 broad.mit.edu 36 19 10324642 10324643 + Missense_Mutation DNP AC AC GG novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 10324642 10324643 TYK2 19 AC AC GG 14 TMEM38A 79041 broad.mit.edu 36 19 16651828 16651828 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 16651828 16651828 TMEM38A 19 C C T 27 RELB 5971 broad.mit.edu 36 19 50217161 50217161 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 50217161 50217161 RELB 19 G G A 48 MATN3 4148 broad.mit.edu 36 2 20069530 20069530 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 20069530 20069530 MATN3 2 C C A 21 RASGRP3 25780 broad.mit.edu 36 2 33622158 33622158 + Missense_Mutation SNP T T C novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33622158 33622158 RASGRP3 2 T T C 64 ITPRIPL1 150771 broad.mit.edu 36 2 96357578 96357578 + Silent SNP C C G novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 96357578 96357578 ITPRIPL1 2 C C G 29 ANKZF1 55139 broad.mit.edu 36 2 219806811 219806811 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 219806811 219806811 ANKZF1 2 G G T 43 MYH7B 57644 broad.mit.edu 36 20 33032158 33032158 + Missense_Mutation SNP A A G novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33032158 33032158 MYH7B 20 A A G 16 TH1L 51497 broad.mit.edu 36 20 56999478 56999478 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56999478 56999478 TH1L 20 G G A 40 SLC17A9 63910 broad.mit.edu 36 20 61067431 61067431 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 61067431 61067431 SLC17A9 20 G G A 40 MKL1 57591 broad.mit.edu 36 22 39155704 39155704 + Silent SNP C C T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 39155704 39155704 MKL1 22 C C T 28 L3MBTL2 83746 broad.mit.edu 36 22 39942158 39942158 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39942158 39942158 L3MBTL2 22 C C A 24 NKTR 4820 broad.mit.edu 36 3 42662461 42662462 + Missense_Mutation DNP GA GA TC novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 42662461 42662462 NKTR 3 GA GA TC 33 SPCS1 28972 broad.mit.edu 36 3 52715333 52715333 + Missense_Mutation SNP C C A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52715333 52715333 SPCS1 3 C C A 25 GTF2E1 2960 broad.mit.edu 36 3 121972336 121972336 + Missense_Mutation SNP C C T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 121972336 121972336 GTF2E1 3 C C T 19 SH3BP2 6452 broad.mit.edu 36 4 2792266 2792267 + Missense_Mutation DNP CA CA AT novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 2792266 2792267 SH3BP2 4 CA CA AT 25 PDGFRA 5156 broad.mit.edu 36 4 54839404 54839404 + Silent SNP C C A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 54839404 54839404 PDGFRA 4 C C A 32 SCLT1 132320 broad.mit.edu 36 4 130140282 130140282 + Missense_Mutation SNP G G C novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 130140282 130140282 SCLT1 4 G G C 48 CYFIP2 26999 broad.mit.edu 36 5 156671363 156671363 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 156671363 156671363 CYFIP2 5 G G T 36 BAK1 578 broad.mit.edu 36 6 33649943 33649943 + Missense_Mutation SNP C C G novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 33649943 33649943 BAK1 6 C C G 26 PKHD1 5314 broad.mit.edu 36 6 51990192 51990192 + Missense_Mutation SNP G G T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 51990192 51990192 PKHD1 6 G G T 41 FHL5 9457 broad.mit.edu 36 6 97158346 97158346 + Missense_Mutation SNP A A C novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 97158346 97158346 FHL5 6 A A C 1 C6orf174 387104 broad.mit.edu 36 6 127839177 127839178 + Missense_Mutation DNP AG AG TA novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 127839177 127839178 C6orf174 6 AG AG TA 3 TAAR2 9287 broad.mit.edu 36 6 132980498 132980498 + Silent SNP G G A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 132980498 132980498 TAAR2 6 G G A 33 NAT1 9 broad.mit.edu 36 8 18124406 18124406 + Silent SNP C C T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 18124406 18124406 NAT1 8 C C T 20 XKR4 114786 broad.mit.edu 36 8 56177895 56177895 + Missense_Mutation SNP T T A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56177895 56177895 XKR4 8 T T A 55 PQBP1 10084 broad.mit.edu 36 X 48643523 48643524 + Splice_Site_SNP DNP GT GT CA novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP DNP 48643523 48643524 PQBP1 23 GT GT CA 44 BCORL1 63035 broad.mit.edu 36 X 128984616 128984616 + Missense_Mutation SNP G G A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128984616 128984616 BCORL1 23 G G A 38 MAGEA5 4104 broad.mit.edu 36 X 151034552 151034552 + Silent SNP C C A novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 151034552 151034552 MAGEA5 23 C C A 17 SRPK3 26576 broad.mit.edu 36 X 152702942 152702942 + Splice_Site_SNP SNP G G C novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 152702942 152702942 SRPK3 23 G G C 34 SRPK3 26576 broad.mit.edu 36 X 152702944 152702944 + Silent SNP A A T novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 152702944 152702944 SRPK3 23 A A T 6 AHNAK2 113146 broad.mit.edu 36 14 104485644 104485680 + Frame_Shift_Del DEL GGCCGGCTCCCTCCGGCACGGGGCCCTCTGGGAGTTT - GGCCGGCTCCCTCCGGCACGGGGCCCTCTGGGAGTTT novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 104485644 104485680 AHNAK2 14 GGCCGGCTCCCTCCGGCACGGGGCCCTCTGGGAGTTT - GGCCGGCTCCCTCCGGCACGGGGCCCTCTGGGAGTTT 35 ABCB11 8647 broad.mit.edu 36 2 169541442 169541451 + Splice_Site_Del DEL TTCTGGAGTG - TTCTGGAGTG novel Unknown TCGA-61-2003-01 TCGA-61-2003-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Splice_Site_Del DEL 169541442 169541451 ABCB11 2 TTCTGGAGTG - TTCTGGAGTG 64