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 CROCC 9696 broad.mit.edu 36 1 17123477 17123477 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 17123477 17123477 CROCC 1 G G C 34 TNNI3K 51086 broad.mit.edu 36 1 74592275 74592275 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 74592275 74592275 TNNI3K 1 G G A 39 CR1 1378 broad.mit.edu 36 1 205856626 205856626 + Missense_Mutation SNP A A G rs55770942 Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 205856626 205856626 CR1 1 A A G 4 TSPAN32 10077 broad.mit.edu 36 11 2295678 2295679 + Missense_Mutation DNP GC GC TG novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 2295678 2295679 TSPAN32 11 GC GC TG 42 EIF4G2 1982 broad.mit.edu 36 11 10777791 10777791 + Missense_Mutation SNP T T G novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 10777791 10777791 EIF4G2 11 T T G 60 CD82 3732 broad.mit.edu 36 11 44583231 44583231 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 44583231 44583231 CD82 11 G G A 40 OR5D13 390142 broad.mit.edu 36 11 55297497 55297497 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 55297497 55297497 OR5D13 11 C C A 25 OR5M11 219487 broad.mit.edu 36 11 56067065 56067065 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 56067065 56067065 OR5M11 11 G G A 37 SRSF8 10929 broad.mit.edu 36 11 94440692 94440692 + Silent SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 94440692 94440692 SRSF8 11 C C T 31 CEP164 22897 broad.mit.edu 36 11 116788066 116788066 + Missense_Mutation SNP A A C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 116788066 116788066 CEP164 11 A A C 6 EI24 9538 broad.mit.edu 36 11 124952674 124952674 + Missense_Mutation SNP T T C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 124952674 124952674 EI24 11 T T C 50 FAM90A1 55138 broad.mit.edu 36 12 8268675 8268675 + Silent SNP G G C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 8268675 8268675 FAM90A1 12 G G C 47 TPH2 121278 broad.mit.edu 36 12 70674491 70674491 + Missense_Mutation SNP C C G novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 C G C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 70674491 70674491 TPH2 12 C C G 17 SLC17A8 246213 broad.mit.edu 36 12 99320298 99320298 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 99320298 99320298 SLC17A8 12 G G T 36 RSRC2 65117 broad.mit.edu 36 12 121572739 121572739 + Nonsense_Mutation SNP T T A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 121572739 121572739 RSRC2 12 T T A 62 FREM2 341640 broad.mit.edu 36 13 38160686 38160686 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38160686 38160686 FREM2 13 C C T 32 C14orf73 91828 broad.mit.edu 36 14 102644578 102644578 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 102644578 102644578 C14orf73 14 G G C 33 KLHL25 64410 broad.mit.edu 36 15 84113931 84113931 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 84113931 84113931 KLHL25 15 G G A 34 ATP2A1 487 broad.mit.edu 36 16 28817150 28817150 + Silent SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 28817150 28817150 ATP2A1 16 G G A 39 FHOD1 29109 broad.mit.edu 36 16 65838667 65838667 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 65838667 65838667 FHOD1 16 G G C 42 PARD6A 50855 broad.mit.edu 36 16 66253794 66253794 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 66253794 66253794 PARD6A 16 C C T 27 RILP 83547 broad.mit.edu 36 17 1496501 1496501 + Silent SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 1496501 1496501 RILP 17 G G A 39 C1QBP 708 broad.mit.edu 36 17 5282175 5282175 + Silent SNP G G C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 5282175 5282175 C1QBP 17 G G C 39 RNF112 7732 broad.mit.edu 36 17 19258701 19258701 + Silent SNP G G T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 19258701 19258701 RNF112 17 G G T 46 GAS2L2 246176 broad.mit.edu 36 17 31100273 31100273 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 31100273 31100273 GAS2L2 17 A A T 6 PLEKHH3 79990 broad.mit.edu 36 17 38079926 38079926 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 38079926 38079926 PLEKHH3 17 G G C 42 PYY 5697 broad.mit.edu 36 17 39386006 39386007 + Missense_Mutation DNP GA GA TG novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 39386006 39386007 PYY 17 GA GA TG 37 MYCBPAP 84073 broad.mit.edu 36 17 45951042 45951042 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 45951042 45951042 MYCBPAP 17 C C T 27 MC2R 4158 broad.mit.edu 36 18 13875322 13875322 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 13875322 13875322 MC2R 18 A A T 3 CEACAM5 1048 broad.mit.edu 36 19 46915842 46915842 + Missense_Mutation SNP T T A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 46915842 46915842 CEACAM5 19 T T A 55 GRLF1 2909 broad.mit.edu 36 19 52117205 52117205 + Nonsense_Mutation SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Nonsense_Mutation SNP 52117205 52117205 GRLF1 19 C C T 27 MYADM 91663 broad.mit.edu 36 19 59069085 59069085 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 59069085 59069085 MYADM 19 G G A 37 PTPRH 5794 broad.mit.edu 36 19 60403629 60403629 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 60403629 60403629 PTPRH 19 C C A 27 GPR113 165082 broad.mit.edu 36 2 26387670 26387670 + Silent SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 26387670 26387670 GPR113 2 G G A 39 TTN 7273 broad.mit.edu 36 2 179105808 179105808 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 179105808 179105808 TTN 2 G G A 38 TTN 7273 broad.mit.edu 36 2 179164298 179164298 + Missense_Mutation SNP A A T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 A T A A Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 179164298 179164298 TTN 2 A A T 12 RQCD1 9125 broad.mit.edu 36 2 219155997 219155997 + Missense_Mutation SNP C C A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 219155997 219155997 RQCD1 2 C C A 17 HUNK 30811 broad.mit.edu 36 21 32290007 32290007 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 32290007 32290007 HUNK 21 C C T 30 GSTT1 2952 broad.mit.edu 36 22 22706834 22706834 + Silent SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 22706834 22706834 GSTT1 22 C C T 23 C3orf20 84077 broad.mit.edu 36 3 14778011 14778011 + Missense_Mutation SNP G G T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 14778011 14778011 C3orf20 3 G G T 47 CADPS 8618 broad.mit.edu 36 3 62714458 62714459 + Missense_Mutation DNP TG TG CA novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation DNP 62714458 62714459 CADPS 3 TG TG CA 51 GBE1 2632 broad.mit.edu 36 3 81668842 81668842 + Silent SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 81668842 81668842 GBE1 3 G G A 40 HTT 3064 broad.mit.edu 36 4 3178152 3178152 + Silent SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 3178152 3178152 HTT 4 C C T 27 FAT4 79633 broad.mit.edu 36 4 126460427 126460427 + Silent SNP T T C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 T C T T Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 126460427 126460427 FAT4 4 T T C 52 FAT4 79633 broad.mit.edu 36 4 126591860 126591860 + Silent SNP C C A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 C A C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 126591860 126591860 FAT4 4 C C A 29 ARL15 54622 broad.mit.edu 36 5 53642036 53642036 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 53642036 53642036 ARL15 5 G G C 33 GRIA1 2890 broad.mit.edu 36 5 153058649 153058649 + Silent SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 153058649 153058649 GRIA1 5 C C T 19 ITK 3702 broad.mit.edu 36 5 156597709 156597709 + Missense_Mutation SNP G G C novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 G C G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 156597709 156597709 ITK 5 G G C 34 TXNDC3 51314 broad.mit.edu 36 7 37883045 37883045 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 37883045 37883045 TXNDC3 7 C C T 28 COL22A1 169044 broad.mit.edu 36 8 139757998 139757998 + Silent SNP C C A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 139757998 139757998 COL22A1 8 C C A 22 KANK1 23189 broad.mit.edu 36 9 702652 702652 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 702652 702652 KANK1 9 G G A 44 COL27A1 85301 broad.mit.edu 36 9 116103804 116103804 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 116103804 116103804 COL27A1 9 C C T 27 ZNF41 7592 broad.mit.edu 36 X 47192031 47192031 + Silent SNP A A G novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 47192031 47192031 ZNF41 23 A A G 6 UBQLN2 29978 broad.mit.edu 36 X 56607115 56607115 + Silent SNP T T G novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Silent SNP 56607115 56607115 UBQLN2 23 T T G 55 ARMCX2 9823 broad.mit.edu 36 X 100798243 100798243 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 C T C C Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 100798243 100798243 ARMCX2 23 C C T 26 UPF3B 65109 broad.mit.edu 36 X 118855948 118855948 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 118855948 118855948 UPF3B 23 G G A 38 ELF4 2000 broad.mit.edu 36 X 129031065 129031065 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 G A G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Missense_Mutation SNP 129031065 129031065 ELF4 23 G G A 42 FMR1 2332 broad.mit.edu 36 X 146832392 146832392 + Missense_Mutation SNP G G A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 146832392 146832392 FMR1 23 G G A 37 L1CAM 3897 broad.mit.edu 36 X 152784006 152784006 + Silent SNP G G T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 G T G G Unknown Valid Somatic x x Sequenom_PCR_WGA x Broad Silent SNP 152784006 152784006 L1CAM 23 G G T 35 GAB3 139716 broad.mit.edu 36 X 153597791 153597791 + Missense_Mutation SNP C C T novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown x x --- x Broad Missense_Mutation SNP 153597791 153597791 GAB3 23 C C T 27 KRT6C 286887 broad.mit.edu 36 12 51153609 51153609 + Frame_Shift_Del DEL A - A rs61740354 Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 51153609 51153609 KRT6C 12 A - A 10 MAP3K9 4293 broad.mit.edu 36 14 70345527 70345529 + In_Frame_Del DEL CCT - CCT novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad In_Frame_Del DEL 70345527 70345529 MAP3K9 14 CCT - CCT 26 PLD2 5338 broad.mit.edu 36 17 4667228 4667229 + Frame_Shift_Del DEL TG - TG novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 - TG TG TG Unknown Valid Somatic Phase_I Capture Illumina GAIIx Broad Frame_Shift_Del DEL 4667228 4667229 PLD2 17 TG - TG 51 TP53 7157 broad.mit.edu 36 17 7520187 7520187 + Frame_Shift_Del DEL A - - novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 - - A A Unknown Valid Somatic Phase_I Capture Illumina GAIIx Broad Frame_Shift_Del DEL 7520187 7520187 TP53 17 A - - 7 C17orf70 80233 broad.mit.edu 36 17 77123352 77123352 + Frame_Shift_Del DEL A - A novel Unknown TCGA-13-1505-01 TCGA-13-1505-10 Unknown Unknown Unknown Phase_I Capture --- Illumina GAIIx Broad Frame_Shift_Del DEL 77123352 77123352 C17orf70 17 A - A 7