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	Trna_tot	Trna_ref	Trna_var	Trna_alt1	Trna_alt2
SSU72	29101	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	1480325	1480325	+	Silent	SNP	C	C	T	rs138912153	alternate_allele	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SSU72-90	NM_014188	exon3	c.G282A	p.R94R	TTCTGGCCGGGGC	.	197	71	265	0	C|1.000;A|0.000	166	100	66	0	0
TMEM52	339456	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	1849335	1849335	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TMEM52-68	NM_178545	exon5	c.C616A	p.P206T	CACCAGGGCTACA	.	150	53	165	1	.	4	1	3	0	0
CELA3B	23436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	22310247	22310247	+	Silent	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CELA3B-91	NM_007352	exon5	c.C423T	p.L141L	CCAGCTCGCCTCA	.	119	38	136	0	.	0	0	0	0	0
ASAP3	55616	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	23759922	23759922	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ASAP3-155	NM_017707	exon21	c.A2123T	p.E708V	ACCTTCTCTTCCT	.	90	47	119	0	.	2	1	1	0	0
CSMD2	114784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	33985175	33985175	+	Silent	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CSMD2-103	NM_052896	exon69	c.A10407T	p.T3469T	GATGTCTGTGGGC	.	235	90	330	0	.	0	0	0	0	0
YBX1	4904	hgsc.bcm.edu	37	1	43166452	43166452	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	YBX1-95	NM_004559	exon7	c.G741A	p.R247R	TTGCAGGGGCCCT	.	24	5	20	1	.	2	2	0	0	0
IGSF3	3321	hgsc.bcm.edu	37	1	117122273	117122273	+	Silent	SNP	G	G	A	rs114783166		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	IGSF3-92	NM_001542	exon11	c.C3135T	p.D1045D	TGGGTCGTCGTCG	.	24	2	33	0	G|1.000;A|0.000	11	11	0	0	0
TTF2	8458	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	117618867	117618867	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TTF2-91	NM_003594	exon6	c.C1341G	p.I447M	ACAAATCCAGGAG	.	48	19	75	0	.	5	2	3	0	0
S100A3	6274	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	153520171	153520171	+	Missense_Mutation	SNP	G	G	C	rs199928185		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	S100A3-90	NM_002960	exon3	c.C293G	p.P98R	GAGCAGGGGGGCT	.	105	52	116	0	G|0.999;C|0.001	2	1	1	0	0
RRNAD1	51093	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	156706431	156706431	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	RRNAD1-90	NM_001142560	exon7	c.T829C	p.C277R	TTTCCATGCTGAG	.	135	52	154	0	.	9	8	1	0	0
PRRC2C	23215	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	171482181	171482181	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	.	NM_015172	exon3	c.C154G	p.R52G	ATTTCACGGCGTA	.	56	20	65	0	.	15	6	9	0	0
TRIM11	81559	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	228584695	228584695	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TRIM11-658	NM_145214	exon5	c.C812A	p.T271N	CACACGGTCCTCA	.	80	35	101	0	.	8	5	3	0	0
NFKB2	4791	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	104158555	104158555	+	Missense_Mutation	SNP	G	G	A	rs45580031	alternate_allele	TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	NFKB2-522	NM_001077494	exon12	c.G1051A	p.G351R	CCCTTCGGGGGTG	.	35	16	54	0	G|0.993;C|0.007	25	15	10	0	0
SMC3	9126	hgsc.bcm.edu	37	10	112342364	112342364	+	Silent	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SMC3-92	NM_005445	exon10	c.A768G	p.L256L	ACAATTAAGAGAT	.	40	2	36	0	.	26	26	0	0	0
TCERG1L	256536	broad.mit.edu	37	10	133058651	133058651	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TCERG1L-138	NM_174937	exon4	c.G727A	p.A243T	CGGCGGCGGTGGC	.	7	2	12	0	.	0	0	0	0	0
TMEM132A	54972	hgsc.bcm.edu	37	11	60702116	60702116	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TMEM132A-227	NM_017870	exon9	c.C1719G	p.D573E	CCCCGACTGGCTG	.	15	2	12	0	.	5	5	0	0	0
CTSC	1075	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	88045694	88045694	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CTSC-90	NM_001814	exon3	c.C347G	p.T116S	CAGTAAGTGGTCA	.	283	119	316	0	.	613	333	280	0	0
MAML2	84441	hgsc.bcm.edu	37	11	95825424	95825424	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	MAML2-850	NM_032427	exon2	c.C1771A	p.Q591K	GCTGCTGTTGCTG	.	6	2	10	2	.	9	9	0	0	0
ROBO3	64221	hgsc.bcm.edu	37	11	124739923	124739923	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ROBO3-113	NM_022370	exon4	c.C725T	p.A242V	ACATGGCGGGAGA	.	59	3	68	0	.	0	0	0	0	0
FGF6	2251	hgsc.bcm.edu	37	12	4554425	4554425	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	FGF6-659	NM_020996	exon1	c.C312T	p.G104G	GATCCGGCCGTCG	.	21	2	39	0	.	0	0	0	0	0
DIP2B	57609	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	51102296	51102296	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	DIP2B-95	NM_173602	exon22	c.C2600A	p.P867H	AAAGACCTGATGC	.	17	9	15	0	.	8	4	4	0	0
LETMD1	25875	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	51450186	51450186	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	LETMD1-90	NM_001243689	exon7	c.G855A	p.L285L	CTTGTTGAGACAT	.	171	71	230	0	.	76	44	32	0	0
OR6C1	390321	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	55714436	55714436	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	OR6C1-69	NM_001005182	exon1	c.A53G	p.D18G	CAGATGACCCAAA	.	119	42	135	1	.	0	0	0	0	0
STAB2	55576	hgsc.bcm.edu	37	12	104139037	104139037	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	STAB2-104	NM_017564	exon57	c.T6118C	p.S2040P	GGCCCCTCGTGTG	.	40	2	28	0	.	0	0	0	0	0
NCOR2	9612	hgsc.bcm.edu	37	12	124887102	124887102	+	Silent	SNP	C	C	T	rs7488825		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	NCOR2-229	NM_006312	exon16	c.G1488A	p.Q496Q	TTGTTGCTGCTGC	.	10	2	12	1	.	0	0	0	0	0
TDRD3	81550	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	61034625	61034625	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TDRD3-516	NM_001146070	exon4	c.G304A	p.G102S	ACTGATGGTCATA	.	111	23	89	0	.	7	6	1	0	0
RALGAPA1	253959	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	36104756	36104756	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	RALGAPA1-138	NM_194301	exon31	c.C4207G	p.P1403A	TTAGAGGTAAGGC	.	33	15	51	0	.	3	2	1	0	0
PSMC6	5706	hgsc.bcm.edu	37	14	53194309	53194309	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	PSMC6-91	NM_002806	exon14	c.T1186G	p.S396A	CTGGAGTCTAAAT	.	85	5	110	0	.	46	46	0	0	0
UBE3A	7337	hgsc.bcm.edu	37	15	25615995	25615995	+	Silent	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	UBE3A-660	NM_000462	exon7	c.T1335C	p.P445P	TTCAAAAGGGATA	.	40	2	58	1	.	9	9	0	0	0
MGA	23269	hgsc.bcm.edu	37	15	42041519	42041519	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	MGA-522	NM_001164273	exon17	c.C5714G	p.S1905C	GGATTTCTCCTCC	.	39	2	66	0	.	8	8	0	0	0
DUOXA2	405753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	45410080	45410080	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	DUOXA2-226	NM_207581	exon6	c.C936A	p.D312E	CCCAGACTTAAAA	.	113	48	140	0	.	0	0	0	0	0
MYO9A	4649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	72172105	72172105	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	MYO9A-93	NM_006901	exon30	c.A5696G	p.E1899G	CGAAATTCCTTCA	.	76	35	88	0	.	5	4	1	0	0
TMEM204	79652	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	1604905	1604905	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TMEM204-90	NM_024600	exon3	c.A559T	p.I187F	ATGCTCATCTGGA	.	85	23	74	0	.	2	2	0	0	0
SCNN1B	6338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	23387095	23387095	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SCNN1B-157	NM_000336	exon8	c.C1189T	p.R397C	ATGATCCGTAACT	.	179	42	124	0	.	0	0	0	0	0
ELMO3	79767	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	67236622	67236622	+	Silent	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ELMO3-90	NM_024712	exon15	c.T1650A	p.T550T	GCTCACTTATGGG	.	69	44	91	0	.	25	6	19	0	0
DEF8	54849	hgsc.bcm.edu;broad.mit.edu	37	16	90023966	90023966	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	DEF8-68	NM_207514	exon5	c.G453A	p.E151E	GATCGAGGAGTGC	.	16	5	14	0	.	56	43	13	0	0
TEKT1	83659	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	17	6703554	6703554	+	Splice_Site	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TEKT1-92	NM_053285	exon9	c.1050-1G>T	.	TTCAATCTAGGAG	.	101	29	82	0	.	0	0	0	0	0
POLR2A	5430	bcgsc.ca	37	17	7402776	7402776	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	POLR2A-91	NM_000937	exon10	c.G1637A	p.R546H	CAGTGCGCAAATT	.	79	5	53	0	.	62	62	0	0	0
RAI1	10743	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	17701717	17701717	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	RAI1-91	NM_030665	exon3	c.G5455A	p.A1819T	GGGGAGGCCCAGG	.	26	17	37	0	.	26	4	22	0	0
ALDH3A2	224	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	19566808	19566808	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ALDH3A2-228	NM_001031806	exon7	c.A1103G	p.H368R	ATAACCATAAGGT	.	82	37	78	0	.	1	1	0	0	0
ASIC2	40	hgsc.bcm.edu	37	17	31618997	31618997	+	Missense_Mutation	SNP	C	C	A	rs112647385		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	.	NM_183377	exon1	c.G137T	p.R46L	AGCGCCCGCTCGC	.	3	3	0	0	C|0.740;A|0.260	0	0	0	0	0
TAF15	8148	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	34171754	34171754	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TAF15-723	NM_139215	exon15	c.G1451A	p.G484D	ATCGAGGTGGCTA	.	36	17	21	0	.	199	68	131	0	0
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305510	39305510	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	KRTAP4-5-90	NM_033188	exon1	c.C510T	p.C170C	GCGGGGGCAGGTG	.	27	3	31	2	.	0	0	0	0	0
HELZ	9931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	65074431	65074431	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	HELZ-92	NM_014877	exon33	c.C5766T	p.L1922L	CTGGAAGAGAGAC	.	124	35	128	0	.	7	4	3	0	0
SLC25A10	1468	broad.mit.edu	37	17	79687107	79687107	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SLC25A10-90	NM_001270888	exon11	c.A891C	p.X297C	ATCCTGACCAGCC	.	80	14	63	9	.	78	74	4	0	0
SMCHD1	23347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	2718194	2718194	+	Nonsense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SMCHD1-46	NM_015295	exon18	c.C2299T	p.Q767X	ATTAGTCAACATG	.	46	19	46	0	.	0	0	0	0	0
TCF4	6925	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	52921812	52921812	+	Silent	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TCF4-523	NM_001243226	exon16	c.T1572C	p.I524I	AGGTCCAATGATT	.	53	22	52	0	.	0	0	0	0	0
APC2	10297	hgsc.bcm.edu	37	19	1460857	1460857	+	Splice_Site	SNP	G	G	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	APC2-290	NM_005883	exon12	c.1521+1G>T	.	CACCAGGTACAGG	.	51	3	66	0	.	11	11	0	0	0
KHSRP	8570	hgsc.bcm.edu	37	19	6420477	6420477	+	Nonsense_Mutation	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	KHSRP-226	NM_003685	exon5	c.C431G	p.S144X	GTCATTGAAGTCC	.	38	2	38	0	.	2	2	0	0	0
FBN3	84467	hgsc.bcm.edu	37	19	8203361	8203361	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	FBN3-100	NM_032447	exon8	c.G953T	p.C318F	TCACAGCAGCACT	.	39	2	60	0	.	0	0	0	0	0
MUC16	94025	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	9056220	9056220	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	MUC16-566	NM_024690	exon3	c.C31226G	p.T10409R	GTCACTGTTCCCA	.	246	94	268	0	.	0	0	0	0	0
CHERP	10523	hgsc.bcm.edu	37	19	16640580	16640580	+	Silent	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CHERP-92	NM_006387	exon8	c.A1008G	p.Q336Q	CTGCTGTTGCTGC	.	38	2	36	1	.	4806	96	4709	0	1
ZNF93	81931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	20044771	20044771	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ZNF93-91	NM_031218	exon4	c.C1007T	p.T336I	TTCATACTGGAGA	.	53	21	53	0	.	28	27	1	0	0
AGBL5	60509	hgsc.bcm.edu	37	2	27291528	27291528	+	Silent	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	AGBL5-154	NM_021831	exon13	c.A2271G	p.G757G	CTCTGGAGACAAA	.	38	2	57	0	.	20	20	0	0	0
SLC8A1	6546	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	40405590	40405590	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SLC8A1-93	NM_021097	exon2	c.A1852G	p.K618E	TGTTTTTCTCATA	.	241	108	270	0	.	0	0	0	0	0
FBXO11	80204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	48049436	48049436	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	FBXO11-659	NM_001190274	exon13	c.T1623G	p.N541K	TATAGAATTTCCC	.	54	19	54	0	.	0	0	0	0	0
CTLA4	1493	hgsc.bcm.edu	37	2	204735645	204735645	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CTLA4-90	NM_005214	exon2	c.T446C	p.I149T	CCCAGATTTATGT	.	39	2	43	0	.	0	0	0	0	0
FRG1B	284802	bcgsc.ca	37	20	29628225	29628225	+	RNA	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	FRG1B-22	NR_003579	exon5	c.529-2A>G	.	TCACTTAGGGGAA	.	261	16	245	6	.	0	0	0	0	0
KCNB1	3745	hgsc.bcm.edu	37	20	48098853	48098853	+	Silent	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	KCNB1-92	NM_004975	exon1	c.G165C	p.T55T	CAGCCGCGTGCGG	.	26	2	26	0	.	1	1	0	0	0
MRGBP	55257	hgsc.bcm.edu	37	20	61427956	61427956	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	.	NM_018270	exon1	c.G81A	p.E27E	GGAGGAGACAGTG	.	5	2	2	0	.	9	4	5	0	0
SYNJ1	8867	hgsc.bcm.edu	37	21	34029042	34029042	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SYNJ1-232	NM_203446	exon21	c.A2867G	p.E956G	AGAAGCTCATCAA	.	38	2	52	0	.	4	4	0	0	0
DNMT3L	29947	hgsc.bcm.edu	37	21	45668957	45668957	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	DNMT3L-228	NM_013369	exon11	c.C947G	p.S316C	TGCAAGGATCCGC	.	28	2	25	0	.	1	1	0	0	0
SBF1	6305	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	50903300	50903300	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SBF1-90	NM_002972	exon13	c.C1379T	p.P460L	CGCTGGGGGTGGT	.	68	25	78	0	.	22	9	13	0	0
VGLL4	9686	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	11600049	11600049	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	VGLL4-91	NM_001128219	exon5	c.C872T	p.S291F	GAGGGGGAGTGAC	.	101	18	97	0	.	64	55	9	0	0
B4GALT4	8702	bcgsc.ca	37	3	118945881	118945881	+	Silent	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	B4GALT4-90	NM_212543	exon5	c.G261A	p.Q87Q	CTTGCTCTGGCCT	.	77	4	60	0	.	0	0	0	0	0
ITGB5	3693	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	124487860	124487860	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ITGB5-227	NM_002213	exon12	c.G2017A	p.V673M	ACTCACCGATGGT	.	101	29	71	0	.	1	0	1	0	0
FGFR3	2261	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	1807787	1807787	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	FGFR3-9542	NM_001163213	exon14	c.A1852G	p.R618G	ATCCACAGGGACC	.	27	11	59	0	.	0	0	0	0	0
SLAIN2	57606	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	48384849	48384849	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	.	NM_020846	exon5	c.T1127A	p.V376E	GTAGAGTGTCCCC	.	46	23	57	0	.	20	12	8	0	0
MANBA	4126	hgsc.bcm.edu	37	4	103590185	103590185	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	MANBA-91	NM_005908	exon10	c.G1252C	p.A418P	CACAGGCAAACAT	.	29	2	36	1	.	14	14	0	0	0
TBCK	93627	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	106967781	106967781	+	Silent	SNP	G	G	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TBCK-336	NM_001163436	exon26	c.C2628T	p.G876G	ATTAATGCCACCA	.	50	15	66	0	.	40	24	16	0	0
LARP7	51574	hgsc.bcm.edu	37	4	113578403	113578403	+	Silent	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	LARP7-93	NM_001267039	exon15	c.T1690C	p.L564L	CTTTAGTTAATCA	.	26	2	40	0	.	2	2	0	0	0
FRG1	2483	hgsc.bcm.edu;broad.mit.edu	37	4	190874221	190874221	+	Splice_Site	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	FRG1-90	NM_004477	exon4	c.260-2A>G	.	TCCAATAGTTGAT	.	62	5	87	0	.	0	0	0	0	0
SLC6A19	340024	hgsc.bcm.edu	37	5	1210657	1210657	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SLC6A19-90	NM_001003841	exon3	c.C442A	p.L148M	GAGCCTCTGCCCT	.	58	3	56	0	.	5	5	0	0	0
JMY	133746	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	78610483	78610483	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	JMY-227	NM_152405	exon9	c.C2468T	p.P823L	CACCACCACCACC	.	20	7	41	0	.	2	1	1	0	0
CHSY3	337876	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	129241299	129241299	+	Silent	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CHSY3-25	NM_175856	exon1	c.C777T	p.R259R	CATGCGCGCCGAC	.	133	40	177	2	.	0	0	0	0	0
RAD50	10111	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	131953819	131953819	+	Silent	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	RAD50-229	NM_005732	exon21	c.A3222G	p.A1074A	TTTGGCATTAGGG	.	249	110	226	0	.	36	16	20	0	0
ZNF346	23567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	176471535	176471535	+	Splice_Site	SNP	G	G	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ZNF346-90	NM_012279	exon4	c.517+1G>C	.	TGGAAGGTACTGG	.	80	28	81	0	.	1	0	1	0	0
ECI2	10455	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	4117677	4117677	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ECI2-90	NM_206836	exon9	c.G894C	p.E298D	AAGCATCTCTGTT	.	83	29	105	0	.	3	3	0	0	0
CDYL	9425	hgsc.bcm.edu	37	6	4891972	4891972	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CDYL-90	NM_004824	exon2	c.A50G	p.K17R	AAAGGAAAAATAA	.	40	2	56	1	.	3	3	0	0	0
TAP1	6890	broad.mit.edu;bcgsc.ca	37	6	32813531	32813531	+	Missense_Mutation	SNP	C	C	G	rs200753447		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TAP1-91	NM_000593	exon11	c.G2252C	p.R751P	GAGTACCGCTCAG	.	46	4	61	0	C|0.999;G|0.001	107	107	0	0	0
TIAM2	26230	bcgsc.ca	37	6	155566798	155566798	+	Silent	SNP	G	G	A	rs201618143		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TIAM2-93	NM_012454	exon18	c.G3585A	p.A1195A	TTACGCGGACCAC	.	270	7	337	0	G|0.999;A|0.001	0	0	0	0	0
WDR27	253769	hgsc.bcm.edu	37	6	170047892	170047892	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	WDR27-69	NM_182552	exon16	c.G1634A	p.R545H	CATACACGTGTGC	.	12	8	7	2	.	7	5	2	0	0
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138738764	138738764	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ZC3HAV1-91	NM_020119	exon11	c.G2265T	p.K755N	TTCAATCTTGAAA	.	50	3	42	0	.	16	16	0	0	0
SGK223	0	hgsc.bcm.edu;broad.mit.edu	37	8	8176328	8176328	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	.	NM_001080826	exon5	c.G3557A	p.G1186D	AGAGTGCCACCAG	.	14	4	15	0	.	2	1	1	0	0
B4GALT1	2683	bcgsc.ca	37	9	33135275	33135275	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	B4GALT1-90	NM_001497	exon2	c.G560A	p.R187Q	TCCTGCCGGTTGC	.	63	4	102	0	.	72	72	0	0	0
AGTPBP1	23287	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	88284416	88284416	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	AGTPBP1-158	NM_015239	exon8	c.A646C	p.N216H	TGGAATTCTTCTT	.	65	26	63	0	.	3	0	3	0	0
CCBL1	883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	131597888	131597888	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	CCBL1-91	NM_001122671	exon10	c.A914T	p.Y305F	ACAAAGTAGCTGC	.	57	23	63	0	.	13	4	9	0	0
LRRC8A	56262	hgsc.bcm.edu	37	9	131670920	131670920	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	LRRC8A-90	NM_001127244	exon3	c.G1477T	p.E493X	CTGCGTGAGAACC	.	33	2	35	0	.	23	23	0	0	0
GPR64	10149	hgsc.bcm.edu	37	X	19026233	19026233	+	Silent	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	GPR64-130	NM_001184834	exon19	c.G1431C	p.L477L	GGTTTCCAGAGAA	.	54	3	103	0	.	0	0	0	0	0
RPS6KA3	6197	hgsc.bcm.edu	37	X	20206637	20206637	+	Silent	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	RPS6KA3-1504	NM_004586	exon8	c.A609G	p.E203E	ACCTTCTTCATCA	.	15	2	32	0	.	21	21	0	0	0
PBDC1	51260	hgsc.bcm.edu	37	X	75394774	75394774	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	.	NM_016500	exon3	c.T146C	p.V49A	CTGAAGTCTATTA	.	39	2	88	0	.	2	2	0	0	0
COL4A6	1288	hgsc.bcm.edu	37	X	107447618	107447618	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	COL4A6-199	NM_001847	exon12	c.G715C	p.A239P	GTCCTGCTGGGCC	.	29	2	67	0	.	2	2	0	0	0
SMG5	23381	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	156221203	156221203	+	Frame_Shift_Del	DEL	G	G	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SMG5-231	NM_015327	exon20	c.2819delC	p.A940fs	.	.	197	69	226	0	.	0	0	0	0	0
SUPT16H	11198	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	14	21821646	21821648	+	Frame_Shift_Del	DEL	CCT	CCT	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	SUPT16H-90	NM_007192	exon25	c.2997_2998del	p.999_1000del	.	.	62	24	109	0	.	0	0	0	0	0
TTN	7273	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	179429832	179429834	+	In_Frame_Del	DEL	AAT	AAT	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	TTN-636	NM_001267550	exon326	c.81025_81027del	p.27009_27009del	.	.	138	58	158	0	.	0	0	0	0	0
AMPH	273	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	38431574	38431574	+	Frame_Shift_Del	DEL	A	A	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	AMPH-95	NM_001635	exon19	c.1653delT	p.H551fs	.	.	90	55	85	0	.	0	0	0	0	0
ASNS	440	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	97482647	97482647	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ASNS-91	NM_133436	exon11	c.1290delG	p.L430fs	.	.	109	25	72	0	.	0	0	0	0	0
ADAM7	8756	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	8	24339727	24339728	+	Frame_Shift_Ins	INS	-	-	TA	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ADAM7-230	NM_003817	exon9	c.778_779insTA	p.L260fs	.	.	101	27	57	0	.	0	0	0	0	0
ZNF585A	199704	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	37642652	37642653	+	Missense_Mutation	DNP	GC	GC	TA	novel		TCGA-A4-8630-01A-11D-2396-08	TCGA-A4-8630-10A-01D-2396-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina HiSeq	80f06506-7e60-402b-8286-dca976db7c76	72b037be-7e9f-4a16-8d05-ee2a4a58247d	.	ZNF585A		exon6	c.G1983T	p.KP716NT	GTAAGGCTTCTCT	.	106.0	46.0	153.0	0.0	.	0	0	0	0	0