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 MTOR 2475 broad.mit.edu 36 1 11195525 11195525 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 11195525 11195525 MTOR 1 C C T 27 HAO2 51179 broad.mit.edu 36 1 119737936 119737936 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 119737936 119737936 HAO2 1 C C T 23 PGLYRP4 57115 broad.mit.edu 36 1 151584458 151584458 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 151584458 151584458 PGLYRP4 1 G G A 40 DCST1 149095 broad.mit.edu 36 1 153280863 153280863 + Silent SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 153280863 153280863 DCST1 1 G G A 34 CHRM3 1131 broad.mit.edu 36 1 238138838 238138838 + Silent SNP A A G novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 238138838 238138838 CHRM3 1 A A G 3 FAM171A1 221061 broad.mit.edu 36 10 15296558 15296558 + Silent SNP A A G novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 15296558 15296558 FAM171A1 10 A A G 7 MYBPC3 4607 broad.mit.edu 36 11 47310321 47310321 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 47310321 47310321 MYBPC3 11 C C T 28 TNKS1BP1 85456 broad.mit.edu 36 11 56837572 56837572 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56837572 56837572 TNKS1BP1 11 C C T 23 HRASLS5 117245 broad.mit.edu 36 11 62990168 62990168 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 62990168 62990168 HRASLS5 11 C C T 23 CLIP1 6249 broad.mit.edu 36 12 121404952 121404952 + Splice_Site_SNP SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 121404952 121404952 CLIP1 12 C C T 18 SCEL 8796 broad.mit.edu 36 13 77074835 77074835 + Missense_Mutation SNP T T A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 77074835 77074835 SCEL 13 T T A 49 SRL 6345 broad.mit.edu 36 16 4182678 4182678 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 4182678 4182678 SRL 16 G G A 39 CDH8 1006 broad.mit.edu 36 16 60412406 60412406 + Missense_Mutation SNP G G C novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 60412406 60412406 CDH8 16 G G C 37 ATP2A3 489 broad.mit.edu 36 17 3797746 3797746 + Silent SNP G G T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 3797746 3797746 ATP2A3 17 G G T 43 TP53 7157 broad.mit.edu 36 17 7518284 7518284 + Missense_Mutation SNP G G A rs28934573 Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 7518284 7518284 TP53 17 G G A 41 MYH1 4619 broad.mit.edu 36 17 10336548 10336548 + Silent SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 10336548 10336548 MYH1 17 G G A 39 MC5R 4161 broad.mit.edu 36 18 13816571 13816571 + Silent SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 13816571 13816571 MC5R 18 C C T 20 DENND1C 79958 broad.mit.edu 36 19 6418577 6418577 + Nonsense_Mutation SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 6418577 6418577 DENND1C 19 G G A 45 CLIP3 25999 broad.mit.edu 36 19 41200677 41200677 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 41200677 41200677 CLIP3 19 C C T 26 INSIG2 51141 broad.mit.edu 36 2 118577263 118577263 + Missense_Mutation SNP C C G novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 118577263 118577263 INSIG2 2 C C G 22 YSK4 80122 broad.mit.edu 36 2 135495793 135495793 + Missense_Mutation SNP T T A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 135495793 135495793 YSK4 2 T T A 64 MYO3B 140469 broad.mit.edu 36 2 170957158 170957158 + Silent SNP A A T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 170957158 170957158 MYO3B 2 A A T 9 FKBP7 51661 broad.mit.edu 36 2 179051426 179051426 + Missense_Mutation SNP T T A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179051426 179051426 FKBP7 2 T T A 49 TTN 7273 broad.mit.edu 36 2 179341743 179341743 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179341743 179341743 TTN 2 G G A 48 MDH1B 130752 broad.mit.edu 36 2 207328020 207328021 + Missense_Mutation DNP CT CT TA novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 207328020 207328021 MDH1B 2 CT CT TA 28 C2orf67 151050 broad.mit.edu 36 2 210597005 210597005 + Silent SNP G G C novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 210597005 210597005 C2orf67 2 G G C 47 EMILIN3 90187 broad.mit.edu 36 20 39423778 39423778 + Silent SNP G G C novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 39423778 39423778 EMILIN3 20 G G C 47 MASP1 5648 broad.mit.edu 36 3 188452221 188452221 + Silent SNP T T C novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 188452221 188452221 MASP1 3 T T C 55 PLEKHG4B 153478 broad.mit.edu 36 5 209195 209195 + Nonsense_Mutation SNP G G T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 209195 209195 PLEKHG4B 5 G G T 37 LIFR 3977 broad.mit.edu 36 5 38559435 38559435 + Missense_Mutation SNP A A T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38559435 38559435 LIFR 5 A A T 4 PLK2 10769 broad.mit.edu 36 5 57787629 57787629 + Missense_Mutation SNP G G C novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 57787629 57787629 PLK2 5 G G C 34 PCDHGA11 56105 broad.mit.edu 36 5 140781683 140781683 + Missense_Mutation SNP T T G novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140781683 140781683 PCDHGA11 5 T T G 51 SLC36A3 285641 broad.mit.edu 36 5 150637392 150637392 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 150637392 150637392 SLC36A3 5 G G A 39 KIAA1191 57179 broad.mit.edu 36 5 175707319 175707319 + Missense_Mutation SNP A A C novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 175707319 175707319 KIAA1191 5 A A C 3 GCM2 9247 broad.mit.edu 36 6 10983140 10983140 + Missense_Mutation SNP G G C novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10983140 10983140 GCM2 6 G G C 45 UBR2 23304 broad.mit.edu 36 6 42758817 42758817 + Missense_Mutation SNP G G T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 42758817 42758817 UBR2 6 G G T 33 C6orf142 90523 broad.mit.edu 36 6 54097511 54097511 + Silent SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 54097511 54097511 C6orf142 6 G G A 40 PDSS2 57107 broad.mit.edu 36 6 107702082 107702082 + Silent SNP A A C novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 107702082 107702082 PDSS2 6 A A C 11 GAL3ST4 79690 broad.mit.edu 36 7 99595804 99595804 + Missense_Mutation SNP C C G novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99595804 99595804 GAL3ST4 7 C C G 32 RELN 5649 broad.mit.edu 36 7 103089058 103089058 + Splice_Site_SNP SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Splice_Site_SNP SNP 103089058 103089058 RELN 7 C C T 18 RHOBTB2 23221 broad.mit.edu 36 8 22920504 22920504 + Silent SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 22920504 22920504 RHOBTB2 8 C C T 19 KCNK9 51305 broad.mit.edu 36 8 140699945 140699945 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 140699945 140699945 KCNK9 8 G G A 38 TRPM3 80036 broad.mit.edu 36 9 72341321 72341321 + Missense_Mutation SNP G G A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 72341321 72341321 TRPM3 9 G G A 38 GNA14 9630 broad.mit.edu 36 9 79228878 79228878 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 79228878 79228878 GNA14 9 C C T 32 PHF2 5253 broad.mit.edu 36 9 95475949 95475949 + Silent SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 95475949 95475949 PHF2 9 C C T 29 ZNF189 7743 broad.mit.edu 36 9 103210725 103210725 + Missense_Mutation SNP A A G novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 103210725 103210725 ZNF189 9 A A G 11 KIAA0649 9858 broad.mit.edu 36 9 137518017 137518017 + Missense_Mutation SNP G G C novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 137518017 137518017 KIAA0649 9 G G C 44 C9orf116 138162 broad.mit.edu 36 9 137527226 137527226 + Missense_Mutation SNP C C A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 137527226 137527226 C9orf116 9 C C A 17 KAL1 3730 broad.mit.edu 36 X 8513413 8513413 + Missense_Mutation SNP T T A novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 8513413 8513413 KAL1 23 T T A 58 MAP3K15 389840 broad.mit.edu 36 X 19290873 19290873 + Missense_Mutation SNP C C G novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 19290873 19290873 MAP3K15 23 C C G 20 FAM47C 442444 broad.mit.edu 36 X 36936626 36936626 + Silent SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 36936626 36936626 FAM47C 23 C C T 19 UPF3B 65109 broad.mit.edu 36 X 118859110 118859110 + Missense_Mutation SNP C C T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 118859110 118859110 UPF3B 23 C C T 32 PSG9 5678 broad.mit.edu 36 19 48463817 48463818 + Frame_Shift_Ins INS - C - novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Ins INS 48463817 48463818 PSG9 19 - C - 54 SAP130 79595 broad.mit.edu 36 2 128470461 128470473 + Frame_Shift_Del DEL GGCTACTCCTCTC - GGCTACTCCTCTC novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 128470461 128470473 SAP130 2 GGCTACTCCTCTC - GGCTACTCCTCTC 35 COL6A6 131873 broad.mit.edu 36 3 131767102 131767120 + Frame_Shift_Del DEL ACACACAGTCTCTGTCTTT - ACACACAGTCTCTGTCTTT novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 131767102 131767120 COL6A6 3 ACACACAGTCTCTGTCTTT - ACACACAGTCTCTGTCTTT 6 ARHGAP18 93663 broad.mit.edu 36 6 130001292 130001292 + Frame_Shift_Del DEL T - T novel Unknown TCGA-24-2254-01 TCGA-24-2254-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 130001292 130001292 ARHGAP18 6 T - T 60