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 RAP1GAP 5909 broad.mit.edu 36 1 21816446 21816446 + Silent SNP G G T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 21816446 21816446 RAP1GAP 1 G G T 47 IQCC 55721 broad.mit.edu 36 1 32445218 32445218 + Silent SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 32445218 32445218 IQCC 1 C C T 26 GLB1L2 89944 broad.mit.edu 36 11 133717917 133717917 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 133717917 133717917 GLB1L2 11 C C T 26 STAB2 55576 broad.mit.edu 36 12 102642987 102642987 + Silent SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 102642987 102642987 STAB2 12 C C T 27 SRRM4 84530 broad.mit.edu 36 12 118052871 118052871 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 118052871 118052871 SRRM4 12 G G A 38 MUDENG 55745 broad.mit.edu 36 14 56822720 56822720 + Silent SNP A A G novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 56822720 56822720 MUDENG 14 A A G 6 DYNC1H1 1778 broad.mit.edu 36 14 101562692 101562692 + Nonsense_Mutation SNP T T A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 101562692 101562692 DYNC1H1 14 T T A 61 ACAN 176 broad.mit.edu 36 15 87218208 87218208 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 87218208 87218208 ACAN 15 C C T 23 WDR90 197335 broad.mit.edu 36 16 645066 645066 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 645066 645066 WDR90 16 G G A 39 PKMYT1 9088 broad.mit.edu 36 16 2964085 2964085 + Silent SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 2964085 2964085 PKMYT1 16 C C T 27 WIPF2 147179 broad.mit.edu 36 17 35670312 35670312 + Splice_Site_SNP SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 35670312 35670312 WIPF2 17 G G A 35 OR7C1 26664 broad.mit.edu 36 19 14771869 14771869 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 14771869 14771869 OR7C1 19 A A G 11 FAM123C 205147 broad.mit.edu 36 2 131237037 131237037 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 131237037 131237037 FAM123C 2 A A T 7 C20orf197 284756 broad.mit.edu 36 20 58079162 58079162 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 58079162 58079162 C20orf197 20 T T C 55 WBP2NL 164684 broad.mit.edu 36 22 40724784 40724784 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 40724784 40724784 WBP2NL 22 A A T 11 SEMA3G 56920 broad.mit.edu 36 3 52450445 52450445 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 52450445 52450445 SEMA3G 3 C C T 27 ST3GAL6 10402 broad.mit.edu 36 3 99993426 99993426 + Missense_Mutation SNP A A G novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 A G A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 99993426 99993426 ST3GAL6 3 A A G 8 CHRD 8646 broad.mit.edu 36 3 185587198 185587198 + Silent SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 185587198 185587198 CHRD 3 G G A 38 MED10 84246 broad.mit.edu 36 5 6425624 6425624 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 6425624 6425624 MED10 5 G G A 42 MAST4 375449 broad.mit.edu 36 5 66386056 66386056 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 66386056 66386056 MAST4 5 C C T 29 KCNN2 3781 broad.mit.edu 36 5 113768427 113768427 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 113768427 113768427 KCNN2 5 G G A 38 UNC5A 90249 broad.mit.edu 36 5 176234015 176234015 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 176234015 176234015 UNC5A 5 G G A 38 FOXC1 2296 broad.mit.edu 36 6 1556120 1556120 + Silent SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 1556120 1556120 FOXC1 6 C C T 25 HIST1H2BK 85236 broad.mit.edu 36 6 27222467 27222467 + Silent SNP G G A rs12207760 Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 27222467 27222467 HIST1H2BK 6 G G A 46 MAS1L 116511 broad.mit.edu 36 6 29562786 29562786 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 29562786 29562786 MAS1L 6 C C T 17 DNAH8 1769 broad.mit.edu 36 6 38949054 38949054 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 38949054 38949054 DNAH8 6 T T C 64 PAPOLB 56903 broad.mit.edu 36 7 4867818 4867818 + Silent SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 4867818 4867818 PAPOLB 7 G G A 37 PRKAR2B 5577 broad.mit.edu 36 7 106574068 106574068 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 106574068 106574068 PRKAR2B 7 G G A 37 ING3 54556 broad.mit.edu 36 7 120396395 120396395 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 120396395 120396395 ING3 7 G G C 35 FLNC 2318 broad.mit.edu 36 7 128272219 128272219 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 128272219 128272219 FLNC 7 C C T 23 ZFHX4 79776 broad.mit.edu 36 8 77928837 77928837 + Silent SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 77928837 77928837 ZFHX4 8 C C T 19 DCAF4L2 138009 broad.mit.edu 36 8 88954868 88954868 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 88954868 88954868 DCAF4L2 8 C C G 25 CBWD1 55871 broad.mit.edu 36 9 168930 168930 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 168930 168930 CBWD1 9 G G C 41 ADAMTSL1 92949 broad.mit.edu 36 9 18564169 18564169 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 18564169 18564169 ADAMTSL1 9 G G A 35 SLC44A1 23446 broad.mit.edu 36 9 107150529 107150529 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 107150529 107150529 SLC44A1 9 G G T 46 PLP1 5354 broad.mit.edu 36 X 102928267 102928267 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 102928267 102928267 PLP1 23 C C T 27 TP53 7157 broad.mit.edu 36 17 7518254 7518254 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Missense_Mutation SNP 7518254 7518254 TP53 17 A A C 12 ITPKB 3707 broad.mit.edu 36 1 224989954 224989956 + In_Frame_Del DEL GAG - GAG novel Unknown TCGA-13-1504-01 TCGA-13-1504-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 224989954 224989956 ITPKB 1 GAG - GAG 45