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	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	COSMIC_Codon	COSMIC_Gene	Transcript_Id	Exon	ChromChange	AAChange	Genome_Plus_Minus_10_Bp	Drug_Target	TTotCov	TVarCov	NTotCov	NVarCov	dbSNPPopFreq	COSMIC_Gene_Freq	COSMIC_Site_Freq	Algorithm
SMARCA5	8467	hgsc.bcm.edu	37	4	144445568	144445571	+	Frame_Shift_Del	DEL	AGAA	AGAA	-	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	AGAA	AGAA	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_003601	exon4	c.467_470del	p.156_157del	.	.	378.0	73.0	367.0	0.0	.	.	.	Atlas-Indel
BAHD1	22893	hgsc.bcm.edu	37	15	40750667	40750668	+	Frame_Shift_Del	DEL	AC	AC	-	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_014952	exon2	c.3_4del	p.1_2del	.	.	90.0	10.0	63.0	0.0	.	.	.	Atlas-Indel
GDF5	8200	hgsc.bcm.edu	37	20	34025393	34025394	+	Frame_Shift_Ins	INS	-	-	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	-	-	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_000557	exon1	c.316_317insA	p.P106fs	.	.	92.0	16.0	58.0	0.0	.	.	.	Pindel,Atlas-Indel
L2HGDH	79944	hgsc.bcm.edu	37	14	50713845	50713847	+	In_Frame_Del	DEL	AGG	AGG	-	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_024884	exon10	c.1322_1324del	p.441_442del	.	.	336.0	53.0	228.0	0.0	.	.	.	Atlas-Indel
KANSL3	55683	hgsc.bcm.edu	37	2	97276835	97276835	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_001115016	exon10	c.G1127A	p.G376E	GGAAACCCAAGGC	.	114.0	20.0	89.0	0.0	.	.	.	Atlas-SNP
USP46	64854	hgsc.bcm.edu	37	4	53492336	53492336	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_022832	exon4	c.A410G	p.Q137R	TCCTCCTGAAGGA	.	168.0	27.0	144.0	0.0	.	.	.	Atlas-SNP
SLC12A3	6559	hgsc.bcm.edu	37	16	56913028	56913028	+	Silent	SNP	A	A	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_001126108	exon10	c.A1224T	p.T408T	TGACACAGTGACC	.	93.0	11.0	74.0	0.0	.	.	.	Atlas-SNP
MTA2	9219	hgsc.bcm.edu	37	11	62365527	62365527	+	Silent	SNP	G	G	A	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_004739	exon6	c.C459T	p.Y153Y	AGCTTGGTATTTG	.	112.0	23.0	128.0	0.0	.	.	.	Atlas-SNP
SMARCA2	6595	hgsc.bcm.edu	37	9	2115838	2115838	+	Missense_Mutation	SNP	A	A	C	rs281875240	alternate_allele	TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_139045	exon25	c.A3473C	p.D1158A	CCCAAGACCGAGC	.	229.0	43.0	199.0	0.0	.	.	.	Atlas-SNP
ZC3H7B	23264	hgsc.bcm.edu	37	22	41742035	41742035	+	Silent	SNP	C	C	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_017590	exon14	c.C1488T	p.Y496Y	TAAGTACGGGGAT	.	56.0	9.0	51.0	0.0	.	.	.	Atlas-SNP
ABT1	29777	hgsc.bcm.edu	37	6	26598339	26598339	+	Splice_Site	SNP	G	G	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_013375	exon2	c.438+1G>T	.	CTCAAGGTGAGAA	.	119.0	18.0	105.0	0.0	.	.	.	Atlas-SNP
SERPINA10	51156	hgsc.bcm.edu	37	14	94756510	94756510	+	Silent	SNP	G	G	A	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_001100607	exon2	c.C421T	p.L141L	AAGGCAGGAGCCC	.	141.0	16.0	135.0	0.0	.	.	.	Atlas-SNP
CD7	924	hgsc.bcm.edu	37	17	80274191	80274191	+	Silent	SNP	C	C	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_006137	exon3	c.G492A	p.P164P	TGTCTGCGGGTCA	.	56.0	6.0	58.0	0.0	.	.	.	Atlas-SNP
BEND6	221336	hgsc.bcm.edu	37	6	56857323	56857323	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	BEND6,NS,carcinoma,0,1	BEND6	NM_152731	exon3	c.C268T	p.R90X	AACAGCCGACTTC	.	138.0	25.0	88.0	0.0	.	0	1	Atlas-SNP
ALPPL2	251	hgsc.bcm.edu	37	2	233271791	233271791	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_031313	exon2	c.G92C	p.W31S	ACTTCTGGAACCG	.	93.0	11.0	80.0	0.0	.	.	.	Atlas-SNP
USP36	57602	hgsc.bcm.edu	37	17	76810500	76810500	+	Silent	SNP	G	G	A	rs139221124	bycluster;byfrequency;by1000genomes	TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_025090	exon11	c.C1158T	p.Y386Y	CTTCACGTAGCAG	.	25.0	5.0	39.0	0.0	0.003	.	.	Atlas-SNP
NMRAL1	57407	hgsc.bcm.edu	37	16	4519318	4519318	+	Silent	SNP	G	G	A	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_020677	exon3	c.C189T	p.V63V	CATGATGACCTGG	.	51.0	12.0	55.0	0.0	.	.	.	Atlas-SNP
XDH	7498	hgsc.bcm.edu	37	2	31602747	31602747	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_000379	exon13	c.C1228T	p.P410S	TGTAGGGGATCTC	.	110.0	23.0	98.0	0.0	.	.	.	Atlas-SNP
FAT4	79633	hgsc.bcm.edu	37	4	126237899	126237899	+	Silent	SNP	T	T	C	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	FAT4_ENST00000394329,larynx,carcinoma,+2,2	FAT4_ENST00000394329	NM_024582	exon1	c.T333C	p.L111L	GGTCCTTTCCAGC	.	51.0	13.0	60.0	0.0	.	+2	2	Atlas-SNP
AHNAK2	113146	hgsc.bcm.edu	37	14	105416870	105416870	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	AHNAK2_ENST00000333244,NS,carcinoma,+2,1	AHNAK2_ENST00000333244	NM_138420	exon7	c.C4918A	p.L1640M	CCTCCAGCTGCGC	.	202.0	40.0	172.0	0.0	.	+2	1	Atlas-SNP
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305800	39305800	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	KRTAP4-5,NS,carcinoma,0,4	KRTAP4-5	NM_033188	exon1	c.A220T	p.S74C	AGCAGCTGGATTC	.	31.0	6.0	29.0	0.0	.	0	4	Atlas-SNP
GPATCH8	23131	hgsc.bcm.edu	37	17	42513867	42513867	+	Silent	SNP	G	G	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_001002909	exon4	c.C240A	p.G80G	ACCCATGCCCATG	.	54.0	10.0	65.0	0.0	.	.	.	Atlas-SNP
NYAP1	222950	hgsc.bcm.edu	37	7	100086782	100086782	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_173564	exon4	c.C1438T	p.P480S	GGTCCACCCCTGG	.	75.0	19.0	54.0	0.0	.	.	.	Atlas-SNP
TPTE2P3	220115	hgsc.bcm.edu	37	13	53095190	53095190	+	RNA	SNP	G	G	C	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	.	.	.	.	GTTTTTGCAGCAG	.	179.0	39.0	216.0	0.0	.	.	.	Atlas-SNP
REV3L	5980	hgsc.bcm.edu	37	6	111804004	111804004	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_002912	exon1	c.G88T	p.A30S	CAGGGGCCTGGGT	.	73.0	18.0	75.0	0.0	.	.	.	Atlas-SNP
PRICKLE2	166336	hgsc.bcm.edu	37	3	64142837	64142837	+	Splice_Site	SNP	C	C	A	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_198859	exon6	c.600+1G>T	.	CTCTAACCTCATC	.	255.0	53.0	220.0	0.0	.	.	.	Atlas-SNP
MRPS5	64969	hgsc.bcm.edu	37	2	95753180	95753180	+	Silent	SNP	T	T	C	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	T	T	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_031902	exon12	c.A1215G	p.K405K	GTCCAGTTTGACG	.	130.0	13.0	113.0	0.0	.	.	.	Atlas-SNP
FAM5C	339479	hgsc.bcm.edu	37	1	190068175	190068175	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	FAM5C,NS,carcinoma,+1,3	FAM5C	NM_199051	exon8	c.C1274G	p.S425W	GTGCACGAGTGCG	.	87.0	5.0	101.0	0.0	.	+1	3	Atlas-SNP
TNS1	7145	hgsc.bcm.edu	37	2	218751314	218751314	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_022648	exon11	c.C547T	p.P183S	ACAAGGGCTTGTT	.	155.0	35.0	98.0	0.0	.	.	.	Atlas-SNP
KCNN3	3782	hgsc.bcm.edu	37	1	154842252	154842252	+	Silent	SNP	A	A	C	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	A	A	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_001204087	exon1	c.T189G	p.P63P	CTGCGGAGGCTGA	.	85.0	14.0	46.0	0.0	.	.	.	Atlas-SNP
RNU6-66	100873770	hgsc.bcm.edu	37	19	46753078	46753078	+	RNA	SNP	C	C	T	rs146564627	by1000genomes	TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	.	.	.	.	CCGGATCATGATC	.	5.0	4.0	7.0	0.0	0.001	.	.	Atlas-SNP
SCRIB	23513	hgsc.bcm.edu	37	8	144893427	144893427	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	SCRIB,larynx,carcinoma,0,1	SCRIB	NM_015356	exon10	c.G995T	p.G332V	CAGCCCCCGATCT	.	81.0	24.0	71.0	0.0	.	0	1	Atlas-SNP
TAS2R8	50836	hgsc.bcm.edu	37	12	10959286	10959286	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	C	C	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	.	.	NM_023918	exon1	c.G294C	p.W98C	GGTAATCCACATA	.	175.0	22.0	96.0	0.0	.	.	.	Atlas-SNP
BMP2K	55589	hgsc.bcm.edu	37	4	79792085	79792085	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-2G-AAKG-05A-11D-A42Y-10	TCGA-2G-AAKG-10A-01D-A433-10	G	G	.	.	.	.	Unknown	Untested	Somatic	.	WXS	none	.	.	Illumina HiSeq	c9c47b6d-b71f-41d0-a5cc-075325b322a6	86018e7d-245a-41de-93d6-ff5b5d81db55	BMP2K_ENST00000502871,NS,carcinoma,0,7	BMP2K_ENST00000502871	NM_017593	exon11	c.G1380C	p.Q460H	TCACCAGCAGCAG	.	50.0	3.0	36.0	0.0	.	0	7	Atlas-SNP
