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 ZNF281 23528 broad.mit.edu 36 1 198643191 198643191 + Missense_Mutation SNP G G T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 198643191 198643191 ZNF281 1 G G T 48 NSUN6 221078 broad.mit.edu 36 10 18977517 18977517 + Missense_Mutation SNP A A T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 18977517 18977517 NSUN6 10 A A T 10 F2 2147 broad.mit.edu 36 11 46706902 46706902 + Missense_Mutation SNP C C T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46706902 46706902 F2 11 C C T 26 SLC43A1 8501 broad.mit.edu 36 11 57025059 57025059 + Silent SNP G G A novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 57025059 57025059 SLC43A1 11 G G A 43 FGF3 2248 broad.mit.edu 36 11 69334464 69334464 + Silent SNP G G A novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 69334464 69334464 FGF3 11 G G A 42 ABCC1 4363 broad.mit.edu 36 16 16104033 16104033 + Missense_Mutation SNP A A G novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 16104033 16104033 ABCC1 16 A A G 4 CD19 930 broad.mit.edu 36 16 28851796 28851796 + Missense_Mutation SNP C C A novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 28851796 28851796 CD19 16 C C A 30 PAPD5 64282 broad.mit.edu 36 16 48819341 48819341 + Missense_Mutation SNP G G C novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 48819341 48819341 PAPD5 16 G G C 41 PCSK4 54760 broad.mit.edu 36 19 1439242 1439242 + Missense_Mutation SNP A A C novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 1439242 1439242 PCSK4 19 A A C 6 RETN 56729 broad.mit.edu 36 19 7640747 7640747 + Silent SNP C C T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 7640747 7640747 RETN 19 C C T 27 SLC7A9 11136 broad.mit.edu 36 19 38046869 38046869 + Missense_Mutation SNP C C G novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38046869 38046869 SLC7A9 19 C C G 17 PAFAH1B3 5050 broad.mit.edu 36 19 47493264 47493264 + Missense_Mutation SNP G G A novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47493264 47493264 PAFAH1B3 19 G G A 37 USP29 57663 broad.mit.edu 36 19 62334010 62334010 + Nonsense_Mutation SNP A A T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 62334010 62334010 USP29 19 A A T 13 HOXD12 3238 broad.mit.edu 36 2 176672933 176672933 + Missense_Mutation SNP C C A novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 176672933 176672933 HOXD12 2 C C A 26 OBSL1 23363 broad.mit.edu 36 2 220129621 220129621 + Missense_Mutation SNP A A C novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 220129621 220129621 OBSL1 2 A A C 2 LPIN3 64900 broad.mit.edu 36 20 39410832 39410832 + Missense_Mutation SNP C C G novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 39410832 39410832 LPIN3 20 C C G 18 SEC61A1 29927 broad.mit.edu 36 3 129271148 129271148 + Missense_Mutation SNP G G T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 129271148 129271148 SEC61A1 3 G G T 40 XRN1 54464 broad.mit.edu 36 3 143534594 143534594 + Missense_Mutation SNP C C T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 143534594 143534594 XRN1 3 C C T 28 SKIL 6498 broad.mit.edu 36 3 171561587 171561587 + Silent SNP T T C novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 171561587 171561587 SKIL 3 T T C 55 ZCCHC4 29063 broad.mit.edu 36 4 24972582 24972582 + Missense_Mutation SNP G G C novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24972582 24972582 ZCCHC4 4 G G C 33 LNX1 84708 broad.mit.edu 36 4 54042704 54042704 + Silent SNP G G A novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 54042704 54042704 LNX1 4 G G A 39 EXOC1 55763 broad.mit.edu 36 4 56421433 56421433 + Missense_Mutation SNP T T C novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56421433 56421433 EXOC1 4 T T C 56 GFOD1 54438 broad.mit.edu 36 6 13473240 13473240 + Missense_Mutation SNP C C T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 13473240 13473240 GFOD1 6 C C T 28 BTN2A1 11120 broad.mit.edu 36 6 26567866 26567866 + Missense_Mutation SNP G G C novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 26567866 26567866 BTN2A1 6 G G C 34 BMP5 653 broad.mit.edu 36 6 55767132 55767132 + Missense_Mutation SNP C C T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55767132 55767132 BMP5 6 C C T 22 TAGAP 117289 broad.mit.edu 36 6 159379141 159379141 + Missense_Mutation SNP G G T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 159379141 159379141 TAGAP 6 G G T 48 TSPAN13 27075 broad.mit.edu 36 7 16784011 16784011 + Missense_Mutation SNP C C G novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 16784011 16784011 TSPAN13 7 C C G 32 ZFHX4 79776 broad.mit.edu 36 8 77929051 77929051 + Nonsense_Mutation SNP C C T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 77929051 77929051 ZFHX4 8 C C T 17 MED22 6837 broad.mit.edu 36 9 135200886 135200886 + Missense_Mutation SNP C C T novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 135200886 135200886 MED22 9 C C T 30 BRD3 8019 broad.mit.edu 36 9 135907364 135907364 + Missense_Mutation SNP T T C novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 135907364 135907364 BRD3 9 T T C 60 RBBP7 5931 broad.mit.edu 36 X 16780622 16780622 + Silent SNP G G A novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown x x --- x Broad Silent SNP 16780622 16780622 RBBP7 23 G G A 37 TP53 7157 broad.mit.edu 36 17 7519249 7519249 + Nonsense_Mutation SNP G G A novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Nonsense_Mutation SNP 7519249 7519249 TP53 17 G G A 47 KLHDC3 116138 broad.mit.edu 36 6 43093652 43093673 + Frame_Shift_Del DEL ATCATGTACATTTTTGGGGGCT - ATCATGTACATTTTTGGGGGCT novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 43093652 43093673 KLHDC3 6 ATCATGTACATTTTTGGGGGCT - ATCATGTACATTTTTGGGGGCT 12 PYCRL 65263 broad.mit.edu 36 8 144759070 144759096 + In_Frame_Del DEL GGCTGCTCGCAGCCCGCCCTGCTCCAG - GGCTGCTCGCAGCCCGCCCTGCTCCAG novel Unknown TCGA-10-0931-01 TCGA-10-0931-11 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 144759070 144759096 PYCRL 8 GGCTGCTCGCAGCCCGCCCTGCTCCAG - GGCTGCTCGCAGCCCGCCCTGCTCCAG 47