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 CASZ1 54897 broad.mit.edu 36 1 10627589 10627589 + Silent SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 10627589 10627589 CASZ1 1 G G A 45 PLA2G2F 64600 broad.mit.edu 36 1 20338596 20338596 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 20338596 20338596 PLA2G2F 1 G G T 43 TARS2 80222 broad.mit.edu 36 1 148737628 148737628 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 148737628 148737628 TARS2 1 C C T 30 OBSCN 84033 broad.mit.edu 36 1 226536469 226536469 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 226536469 226536469 OBSCN 1 G G A 46 ANKRD30A 91074 broad.mit.edu 36 10 37548593 37548593 + Missense_Mutation SNP A A C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37548593 37548593 ANKRD30A 10 A A C 7 RASGEF1A 221002 broad.mit.edu 36 10 43016152 43016152 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43016152 43016152 RASGEF1A 10 A A G 6 FAM190B 54462 broad.mit.edu 36 10 86121660 86121660 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 86121660 86121660 FAM190B 10 A A G 4 C10orf96 374355 broad.mit.edu 36 10 118091583 118091583 + Missense_Mutation SNP A A C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 118091583 118091583 C10orf96 10 A A C 13 OR5F1 338674 broad.mit.edu 36 11 55518352 55518352 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55518352 55518352 OR5F1 11 G G T 48 ZBTB3 79842 broad.mit.edu 36 11 62278032 62278032 + Nonsense_Mutation SNP C C A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 62278032 62278032 ZBTB3 11 C C A 21 TCIRG1 10312 broad.mit.edu 36 11 67569068 67569068 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 67569068 67569068 TCIRG1 11 G G T 38 EED 8726 broad.mit.edu 36 11 85639051 85639051 + Silent SNP A A G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 85639051 85639051 EED 11 A A G 5 ME3 10873 broad.mit.edu 36 11 85835783 85835783 + Missense_Mutation SNP G G C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 85835783 85835783 ME3 11 G G C 40 MMP27 64066 broad.mit.edu 36 11 102078699 102078699 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 102078699 102078699 MMP27 11 C C T 30 CD4 920 broad.mit.edu 36 12 6796678 6796678 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6796678 6796678 CD4 12 G G T 43 PTHLH 5744 broad.mit.edu 36 12 28007615 28007615 + Missense_Mutation SNP T T C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28007615 28007615 PTHLH 12 T T C 58 PFKM 5213 broad.mit.edu 36 12 46815382 46815382 + Silent SNP C C G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 46815382 46815382 PFKM 12 C C G 32 C12orf56 115749 broad.mit.edu 36 12 62955010 62955010 + Missense_Mutation SNP A A C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 62955010 62955010 C12orf56 12 A A C 4 PABPC3 5042 broad.mit.edu 36 13 24568542 24568542 + Missense_Mutation SNP T T G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 24568542 24568542 PABPC3 13 T T G 55 HSPH1 10808 broad.mit.edu 36 13 30624998 30624998 + Missense_Mutation SNP T T A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 30624998 30624998 HSPH1 13 T T A 51 FREM2 341640 broad.mit.edu 36 13 38160554 38160554 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38160554 38160554 FREM2 13 A A G 2 SCEL 8796 broad.mit.edu 36 13 77074235 77074235 + Nonsense_Mutation SNP C C T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 77074235 77074235 SCEL 13 C C T 29 GMPR2 51292 broad.mit.edu 36 14 23777318 23777318 + Missense_Mutation SNP G G C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 23777318 23777318 GMPR2 14 G G C 43 TGM1 7051 broad.mit.edu 36 14 23800742 23800743 + Missense_Mutation DNP GA GA AT novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 23800742 23800743 TGM1 14 GA GA AT 37 XRCC3 7517 broad.mit.edu 36 14 103247142 103247142 + Missense_Mutation SNP A A C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 103247142 103247142 XRCC3 14 A A C 13 CPNE2 221184 broad.mit.edu 36 16 55702215 55702215 + Missense_Mutation SNP G G C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55702215 55702215 CPNE2 16 G G C 36 EDC4 23644 broad.mit.edu 36 16 66470523 66470523 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 66470523 66470523 EDC4 16 A A G 1 NFATC3 4775 broad.mit.edu 36 16 66817872 66817872 + Silent SNP C C A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 66817872 66817872 NFATC3 16 C C A 32 MPP2 4355 broad.mit.edu 36 17 39312259 39312259 + Nonsense_Mutation SNP G G C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 39312259 39312259 MPP2 17 G G C 40 MAPT 4137 broad.mit.edu 36 17 41457217 41457217 + Silent SNP C C T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 41457217 41457217 MAPT 17 C C T 18 TSEN54 283989 broad.mit.edu 36 17 71031999 71031999 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 71031999 71031999 TSEN54 17 G G T 48 DSG3 1830 broad.mit.edu 36 18 27293046 27293046 + Missense_Mutation SNP T T C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 27293046 27293046 DSG3 18 T T C 49 LMAN1 3998 broad.mit.edu 36 18 55177244 55177244 + Silent SNP C C A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 55177244 55177244 LMAN1 18 C C A 30 RFX1 5989 broad.mit.edu 36 19 13940457 13940457 + Missense_Mutation SNP T T G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 13940457 13940457 RFX1 19 T T G 60 KIRREL2 84063 broad.mit.edu 36 19 41049062 41049062 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 41049062 41049062 KIRREL2 19 G G A 46 RYR1 6261 broad.mit.edu 36 19 43755730 43755730 + Missense_Mutation SNP A A T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 43755730 43755730 RYR1 19 A A T 11 FCGBP 8857 broad.mit.edu 36 19 45060417 45060417 + Silent SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 45060417 45060417 FCGBP 19 G G A 40 POU2F2 5452 broad.mit.edu 36 19 47288114 47288114 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47288114 47288114 POU2F2 19 G G T 42 B3GALT1 8708 broad.mit.edu 36 2 168434166 168434166 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 168434166 168434166 B3GALT1 2 C C A 24 DOCK10 55619 broad.mit.edu 36 2 225377139 225377139 + Missense_Mutation SNP G G T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 225377139 225377139 DOCK10 2 G G T 44 SH3BP4 23677 broad.mit.edu 36 2 235615757 235615757 + Silent SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 235615757 235615757 SH3BP4 2 G G A 35 GAS2L1 10634 broad.mit.edu 36 22 28037913 28037913 + Missense_Mutation SNP C C A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 28037913 28037913 GAS2L1 22 C C A 21 SI 6476 broad.mit.edu 36 3 166265802 166265802 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 166265802 166265802 SI 3 G G A 37 PELO 53918 broad.mit.edu 36 5 52132066 52132066 + Nonsense_Mutation SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 52132066 52132066 PELO 5 G G A 42 FAM53C 51307 broad.mit.edu 36 5 137710422 137710422 + Missense_Mutation SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 137710422 137710422 FAM53C 5 G G A 44 KDM3B 51780 broad.mit.edu 36 5 137755763 137755763 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 137755763 137755763 KDM3B 5 A A G 4 PCDH12 51294 broad.mit.edu 36 5 141317388 141317388 + Silent SNP C C G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 141317388 141317388 PCDH12 5 C C G 25 GALNT10 55568 broad.mit.edu 36 5 153769293 153769293 + Splice_Site_SNP SNP G G T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 153769293 153769293 GALNT10 5 G G T 33 GCM1 8521 broad.mit.edu 36 6 53104763 53104763 + Splice_Site_SNP SNP C C A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 53104763 53104763 GCM1 6 C C A 18 ANKRD6 22881 broad.mit.edu 36 6 90383054 90383054 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 90383054 90383054 ANKRD6 6 A A G 1 AHI1 54806 broad.mit.edu 36 6 135829182 135829182 + Missense_Mutation SNP A A G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 135829182 135829182 AHI1 6 A A G 3 IPCEF1 26034 broad.mit.edu 36 6 154628743 154628743 + Missense_Mutation SNP C C T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 154628743 154628743 IPCEF1 6 C C T 25 THSD7A 221981 broad.mit.edu 36 7 11385794 11385794 + Silent SNP C C G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 11385794 11385794 THSD7A 7 C C G 19 ZMIZ2 83637 broad.mit.edu 36 7 44765470 44765470 + Silent SNP C C T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 44765470 44765470 ZMIZ2 7 C C T 21 SPAM1 6677 broad.mit.edu 36 7 123380877 123380877 + Missense_Mutation SNP T T G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 T G T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 123380877 123380877 SPAM1 7 T T G 62 EPPK1 83481 broad.mit.edu 36 8 145012717 145012717 + Silent SNP C C T novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 145012717 145012717 EPPK1 8 C C T 25 OPLAH 26873 broad.mit.edu 36 8 145186837 145186837 + Silent SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 145186837 145186837 OPLAH 8 G G A 40 GPR34 2857 broad.mit.edu 36 X 41440897 41440897 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 41440897 41440897 GPR34 23 C C G 20 FAAH2 158584 broad.mit.edu 36 X 57490193 57490193 + Silent SNP C C G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 57490193 57490193 FAAH2 23 C C G 21 FAM123B 139285 broad.mit.edu 36 X 63326941 63326941 + Missense_Mutation SNP G G C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 63326941 63326941 FAM123B 23 G G C 41 TAF1 6872 broad.mit.edu 36 X 70514835 70514835 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 70514835 70514835 TAF1 23 C C G 30 TCEAL2 140597 broad.mit.edu 36 X 101268629 101268629 + Silent SNP G G A novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 101268629 101268629 TCEAL2 23 G G A 40 TFDP3 51270 broad.mit.edu 36 X 132179527 132179527 + Missense_Mutation SNP C C G novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 132179527 132179527 TFDP3 23 C C G 28 MAGEA3 4102 broad.mit.edu 36 X 151686585 151686585 + Missense_Mutation SNP A A C novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 151686585 151686585 MAGEA3 23 A A C 7 TP53 7157 broad.mit.edu 36 17 7519000 7519002 + In_Frame_Del DEL GAG GAG - novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 7519000 7519002 TP53 17 GAG GAG - 45 PSTPIP1 9051 broad.mit.edu 36 15 75116508 75116509 + Frame_Shift_Ins INS - AAGT AAGT novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 75116508 75116509 PSTPIP1 15 - AAGT AAGT 47 ITFG3 83986 broad.mit.edu 36 16 253326 253333 + Frame_Shift_Del DEL GGCTCAGA - GGCTCAGA novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 253326 253333 ITFG3 16 GGCTCAGA - GGCTCAGA 43 ZFPM1 161882 broad.mit.edu 36 16 87128758 87128767 + Frame_Shift_Del DEL CGCCGGCGCC - CGCCGGCGCC novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 87128758 87128767 ZFPM1 16 CGCCGGCGCC - CGCCGGCGCC 19 SON 6651 broad.mit.edu 36 21 33847489 33847492 + Frame_Shift_Del DEL AGTC - AGTC novel Unknown TCGA-24-0975-01 TCGA-24-0975-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 33847489 33847492 SON 21 AGTC - AGTC 11