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
PTCHD2	57540	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	11561189	11561189	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PTCHD2-209	NM_020780	exon2	c.G140A	p.R47Q	GCTGGCGGCACTG	.	64	57	51	0	.	2	0	2	0	0
MRPL37	51253	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	1	54678298	54678298	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	MRPL37-90	NM_016491	exon5	c.C957T	p.G319G	TTTTGGCAGTGCC	.	91	78	95	0	.	45	5	40	0	0
IGSF3	3321	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	1	117150771	117150771	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	IGSF3-92	NM_001007237	exon5	c.G1015A	p.E339K	CAAATTCGCTGTT	.	162	120	186	0	.	3	0	3	0	0
HRNR	388697	bcgsc.ca	37	1	152188999	152188999	+	Silent	SNP	G	G	A	rs149648668	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	HRNR-93	NM_001009931	exon3	c.C5106T	p.H1702H	TCGGCCGTGGCCC	.	231	66	402	24	G|0.947;A|0.053	0	0	0	0	0
HRNR	388697	bcgsc.ca	37	1	152189038	152189038	+	Silent	SNP	A	A	G	rs145118416	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	HRNR-93	NM_001009931	exon3	c.T5067C	p.Y1689Y	CTGACCATAGCGG	.	157	53	272	15	A|0.968;G|0.032	0	0	0	0	0
CD1A	909	broad.mit.edu	37	1	158224501	158224501	+	Silent	SNP	T	T	G	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CD1A-93	NM_001763	exon1	c.T42G	p.G14G	CCCAGGTGATGGC	.	155	5	124	3	.	0	0	0	0	0
CR1	1378	broad.mit.edu	37	1	207787753	207787753	+	Nonsense_Mutation	SNP	C	C	T	rs55749440		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CR1-93	NM_000651	exon40	c.C6580T	p.R2194X	AGGTTCCGATTAA	.	247	11	167	0	.	0	0	0	0	0
NEK2	4751	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	211846871	211846871	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	NEK2-765	NM_001204183	exon3	c.C509T	p.T170M	AAACTCGTGTCAT	.	205	43	154	0	.	0	0	0	0	0
IBA57	200205	broad.mit.edu	37	1	228362441	228362441	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	IBA57-90	NM_001010867	exon2	c.C390A	p.S130R	TGACAGCTCGGTG	.	80	13	18	1	.	5	5	0	0	0
NFKB2	4791	hgsc.bcm.edu	37	10	104159196	104159196	+	Silent	SNP	A	A	G	rs4919633	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	NFKB2-522	NM_001077494	exon13	c.A1269G	p.P423P	GGAGCCAAGCGCC	.	14	14	0	0	A|0.009;G|0.991	23	0	23	0	0
TAF5	6877	hgsc.bcm.edu	37	10	105128134	105128134	+	Missense_Mutation	SNP	T	T	G	rs10883859	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	TAF5-92	NM_006951	exon1	c.T388G	p.S130A	GCGGGCTCCGGAG	.	24	8	1	0	T|0.623;G|0.377	0	0	0	0	0
GFRA1	2674	broad.mit.edu;bcgsc.ca	37	10	117884831	117884831	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	GFRA1-93	NM_005264	exon6	c.G671A	p.R224Q	CGCCTCCGCTCTG	.	228	10	140	0	.	0	0	0	0	0
MUC6	4588	bcgsc.ca	37	11	1016835	1016835	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	MUC6-23	NM_005961	exon31	c.T5966C	p.F1989S	GTCTGGAAGGATG	.	2350	73	2602	38	.	3	3	0	0	0
MUC2	4583	broad.mit.edu	37	11	1092940	1092940	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	MUC2-90	NM_002457	exon30	c.A4759T	p.T1587S	CCCATCACCACCA	.	97	7	99	0	.	0	0	0	0	0
MUC5B	727897	bcgsc.ca	37	11	1266716	1266716	+	Missense_Mutation	SNP	T	T	C	rs80150964		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_002458	exon31	c.T8606C	p.M2869T	TGACCATGGGCTG	.	92	36	136	0	C|1.000;|0.000	0	0	0	0	0
OR8H2	390151	broad.mit.edu	37	11	55872537	55872537	+	Missense_Mutation	SNP	A	A	G	rs61746549	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	OR8H2-70	NM_001005200	exon1	c.A19G	p.N7D	AGGAATAACACAA	.	110	6	129	1	A|0.999;G|0.001	0	0	0	0	0
GAL3ST3	89792	hgsc.bcm.edu	37	11	65810209	65810209	+	Silent	SNP	C	C	T	rs61895584	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	GAL3ST3-91	NM_033036	exon3	c.G1065A	p.P355P	CTGCCACGGCTGC	.	4	4	0	0	C|0.233;T|0.767	0	0	0	0	0
KLC2	64837	broad.mit.edu	37	11	66033423	66033423	+	Silent	SNP	T	T	G	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	KLC2-90	NM_022822	exon13	c.T1542G	p.G514G	TGGGGGTGCCGGG	.	127	24	143	11	.	44	43	1	0	0
B3GNT6	192134	hgsc.bcm.edu	37	11	76751542	76751542	+	Splice_Site	DEL	T	T	-	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_138706	exon2	c.946+1T>-	.	TGTGTCTTGGAGC	.	12	12	0	0	.	0	0	0	0	0
LRP6	4040	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	12301919	12301919	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	LRP6-661	NM_002336	exon14	c.G3163A	p.E1055K	CCTGCTCGCCTTT	.	205	12	150	0	.	12	11	1	0	0
KIF5A	3798	broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	57957244	57957244	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	KIF5A-517	NM_004984	exon2	c.G152A	p.R51H	TTGACCGTGTATT	.	256	32	170	1	.	0	0	0	0	0
RAB21	23011	ucsc.edu	37	12	72164383	72164383	+	Silent	SNP	T	T	G	rs201148269	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	RAB21-227	NM_014999	exon3	c.T231G	p.G77G	GGCAGGTCAAGAG	.	81	21	47	5	T|0.962;G|0.038	0	0	0	0	0
BBS10	79738	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	76741456	76741459	+	Frame_Shift_Del	DEL	TCTG	TCTG	-	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	TCTG	TCTG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	BBS10-92	NM_024685	exon2	c.306_309del	p.102_103del	CTTTTCTCTGTCT	.	110	48	58	0	.	0	0	0	0	0
RNFT2	84900	hgsc.bcm.edu	37	12	117187907	117187907	+	Silent	SNP	T	T	C	rs111256849	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_001109903	exon4	c.T345C	p.H115H	CCACCATTTCCAC	.	24	9	3	0	T|0.767;C|0.233	1	1	0	0	0
SUGT1	10910	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	13	53237236	53237236	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SUGT1-226	NM_001130912	exon8	c.G484T	p.E162X	GGCTCAGAATCTG	.	45	13	54	0	.	0	0	0	0	0
OR10G3	26533	bcgsc.ca	37	14	22038525	22038525	+	Silent	SNP	G	G	T	rs11626693	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	OR10G3-68	NM_001005465	exon1	c.C351A	p.T117T	CATTAGGGTGTAG	.	215	9	205	2	G|0.656;T|0.344	0	0	0	0	0
HECTD1	25831	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	31598273	31598273	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	HECTD1-570	NM_015382	exon25	c.T4304A	p.V1435D	TGAGGGACGTTTT	.	217	167	261	1	.	22	5	17	0	0
PLEK2	26499	bcgsc.ca	37	14	67878765	67878765	+	Silent	SNP	G	G	A	rs115017102	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PLEK2-92	NM_016445	exon1	c.C12T	p.G4G	GAGCACGCCGTCC	.	27	25	11	1	G|0.976;A|0.024	12	0	12	0	0
SEMA6D	80031	bcgsc.ca	37	15	48053888	48053888	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SEMA6D-138	NM_153617	exon7	c.A478G	p.I160V	GAAGAAATTAGTG	.	77	4	93	0	.	1	1	0	0	0
TLN2	83660	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	63017231	63017231	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	TLN2-573	NM_015059	exon24	c.G3183A	p.T1061T	GCAGACGCTTAAG	.	43	7	45	0	.	3	3	0	0	0
KBTBD13	390594	hgsc.bcm.edu	37	15	65369395	65369395	+	Missense_Mutation	SNP	C	C	T	rs2919358	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_001101362	exon1	c.C242T	p.A81V	TGCAGGCCGTGGA	.	7	7	2	0	C|0.452;T|0.548	0	0	0	0	0
FAM173A	65990	broad.mit.edu	37	16	771612	771612	+	Silent	SNP	C	C	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	FAM173A-91	NM_001271285	exon2	c.C177A	p.G59G	CGTCGGCGCGAGC	.	57	8	24	1	.	3	3	0	0	0
NDUFB10	4716	broad.mit.edu	37	16	2011627	2011645	+	Frame_Shift_Del	DEL	CCAGGACCGCTGTGCGTGC	CCAGGACCGCTGTGCGTGC	-	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	NDUFB10-90	NM_004548	exon3	c.399_409del	p.133_137del	GGCCTACCAGGAC	.	15	4	16	0	.	0	0	0	0	0
SLC9A3R2	9351	broad.mit.edu	37	16	2086730	2086730	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SLC9A3R2-23	NM_004785	exon4	c.T596G	p.V199G	GGCAGGTGAACGG	.	70	24	56	10	.	0	0	0	0	0
ANKS3	124401	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	4747041	4747041	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ANKS3-90	NM_133450	exon17	c.G1959C	p.W653C	CTCCCGCCACTTC	.	69	48	96	1	.	12	1	11	0	0
CLEC16A	23274	hgsc.bcm.edu	37	16	11272460	11272460	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CLEC16A-92	NM_015226	exon23	c.C3075T	p.P1025P	CATGCCCCCGCTG	.	29	22	2	0	.	18	1	17	0	0
CCDC102A	92922	hgsc.bcm.edu	37	16	57562804	57562804	+	Missense_Mutation	SNP	G	G	A	rs12935069		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CCDC102A-91	NM_033212	exon2	c.C286T	p.R96W	ACCACCGGCGCAT	.	9	9	0	0	G|0.001;A|0.999	1	0	1	0	0
ZFPM1	161882	hgsc.bcm.edu	37	16	88599696	88599697	+	Frame_Shift_Del	DEL	GA	GA	-	rs67549438	alternate_allele	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	GA	GA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ZFPM1-90	NM_153813	exon10	c.1330_1331del	p.444_444del	AGAGCGGAGCCTC	.	19	13	0	0	.	0	0	0	0	0
ZFPM1	161882	hgsc.bcm.edu	37	16	88599697	88599705	+	In_Frame_Del	DEL	AGCCTCTGG	AGCCTCTGG	-	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	AGCCTCTGG	AGCCTCTGG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ZFPM1-90	NM_153813	exon10	c.1331_1339del	p.444_447del	GAGCGGAGCCTCT	.	18	0	0	0	.	0	0	0	0	0
ZFPM1	161882	hgsc.bcm.edu	37	16	88599701	88599701	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ZFPM1-90	NM_153813	exon10	c.1335delT	p.P445fs	GGAGCCTCTGGCC	.	17	14	0	0	.	0	0	0	0	0
ZFPM1	161882	hgsc.bcm.edu	37	16	88599703	88599705	+	In_Frame_Del	DEL	TGG	TGG	-	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	TGG	TGG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ZFPM1-90	NM_153813	exon10	c.1337_1339del	p.446_447del	AGCCTCTGGCCCA	.	17	14	0	0	.	0	0	0	0	0
C16orf3	750	bcgsc.ca	37	16	90095573	90095573	+	Missense_Mutation	SNP	C	C	T	rs77382359		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	C16orf3-90	NM_001214	exon1	c.G178A	p.V60I	AGGCTACGGGGCA	.	48	13	59	0	C|0.500;T|0.500	0	0	0	0	0
TP53	7157	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	7578415	7578428	+	Frame_Shift_Del	DEL	ACCTCCGTCATGTG	ACCTCCGTCATGTG	-	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	ACCTCCGTCATGTG	ACCTCCGTCATGTG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	TP53-70225	NM_000546	exon5	c.502_515del	p.168_172del	CTCACAACCTCCG	.	55	26	111	0	.	0	0	0	0	0
TVP23C	201158	ucsc.edu	37	17	15457087	15457087	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_145301	exon3	c.G152A	p.C51Y	AGAAGACAGACGA	.	239	10	293	10	.	111	13	98	0	0
SARM1	23098	hgsc.bcm.edu	37	17	26699121	26699121	+	Missense_Mutation	SNP	G	G	C	rs7212814		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_015077	exon1	c.G68C	p.R23P	CACGGCGGGGCGC	.	8	8	0	0	G|0.001;C|0.999	4	0	4	0	0
FAM222B	55731	broad.mit.edu	37	17	27085450	27085450	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_018182	exon4	c.C1527A	p.S509R	CATCAAGCTGTTC	.	58	3	61	0	.	21	21	0	0	0
SEZ6	124925	ucsc.edu	37	17	27286750	27286750	+	Silent	SNP	G	G	A	rs9907950	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SEZ6-90	NM_001098635	exon8	c.C1737T	p.D579D	CTGGGGGTCGTGG	.	47	4	70	1	G|0.841;A|0.159	0	0	0	0	0
LAMA3	3909	ucsc.edu;bcgsc.ca	37	18	21464756	21464756	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	LAMA3-100	NM_001127717	exon41	c.G5242T	p.V1748L	TGTGTGGTGAATG	.	43	4	46	0	.	0	0	0	0	0
ARID3A	1820	hgsc.bcm.edu	37	19	929678	929678	+	Silent	SNP	G	G	A	rs3826948		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ARID3A-90	NM_005224	exon2	c.G150A	p.E50E	GCCCGAGAGTGCC	.	5	5	0	0	T|0.495;C|0.504	1	0	1	0	0
ARID3A	1820	hgsc.bcm.edu	37	19	929753	929753	+	Silent	SNP	A	A	G	rs1799595		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ARID3A-90	NM_005224	exon2	c.A225G	p.P75P	ACACCCAGCCAGC	.	12	12	0	0	A|0.114;G|0.886	2	0	2	0	0
PDE4C	5143	ucsc.edu	37	19	18331699	18331699	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PDE4C-94	NM_000923	exon6	c.C580A	p.Q194K	GGAGCTGATTGCT	.	41	4	68	0	.	0	0	0	0	0
RINL	126432	hgsc.bcm.edu	37	19	39360720	39360720	+	Missense_Mutation	SNP	G	G	A	rs8110393		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	RINL-91	NM_001195833	exon9	c.C1205T	p.P402L	GGGGCGGGGCTCT	.	13	12	1	0	G|0.349;A|0.651	0	0	0	0	0
ZNF230	7773	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	44515611	44515611	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ZNF230-90	NM_006300	exon5	c.A1420T	p.M474L	AATGATATGTAAG	.	18	6	15	0	.	4	4	0	0	0
TPRX1	284355	broad.mit.edu	37	19	48305622	48305622	+	Missense_Mutation	SNP	A	A	G	rs201007421		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	TPRX1-90	NM_198479	exon2	c.T646C	p.S216P	GGCCTGAGATTGG	.	25	4	26	2	.	1	1	0	0	0
NTN5	126147	hgsc.bcm.edu	37	19	49164952	49164952	+	Silent	SNP	A	A	G	rs281392	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	NTN5-136	NM_145807	exon7	c.T1452C	p.S484S	CCTGGGACTGGGT	.	4	4	2	0	A|0.464;G|0.536	0	0	0	0	0
IZUMO1	284359	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	49245556	49245556	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	IZUMO1-91	NM_182575	exon7	c.G510A	p.V170V	AACTTCCACATTC	.	94	75	99	0	.	5	0	5	0	0
ZNF628	89887	hgsc.bcm.edu	37	19	55993260	55993260	+	Missense_Mutation	SNP	A	A	G	rs34864744		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ZNF628-22	NM_033113	exon3	c.A700G	p.T234A	CCGGGTACCGCCT	.	5	5	0	0	A|0.270;G|0.730	1	0	1	0	0
ZNF787	126208	hgsc.bcm.edu	37	19	56599438	56599440	+	In_Frame_Del	DEL	TCG	TCG	-	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	TCG	TCG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ZNF787-69	NM_001002836	exon3	c.1101_1103del	p.367_368del	GCGGCCTCGTCGT	.	10	10	0	0	.	0	0	0	0	0
ZNF814	730051	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	58385748	58385748	+	Missense_Mutation	SNP	G	G	A	rs145250945		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_001144989	exon3	c.C1010T	p.A337V	AAGCTAGCATATT	.	175	66	85	0	.	3	3	0	0	0
ZNF814	730051	broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	58385762	58385762	+	Silent	SNP	C	C	G	rs199732634		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_001144989	exon3	c.G996C	p.S332S	GCTAAACGATTTC	.	158	52	80	1	.	3	3	0	0	0
ATL2	64225	bcgsc.ca;mdanderson.org	37	2	38604351	38604351	+	Missense_Mutation	SNP	A	A	G	rs3731847	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ATL2-228	NM_001135673	exon1	c.T52C	p.W18R	GGCGCCACAGCCC	.	116	103	24	1	A|0.523;G|0.477	38	0	38	0	0
WDPCP	51057	broad.mit.edu	37	2	63631285	63631285	+	Missense_Mutation	SNP	C	C	G	rs61734466	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	WDPCP-91	NM_015910	exon10	c.G1333C	p.A445P	GAGGAGCTATCCA	.	128	4	115	0	C|0.975;G|0.025	6	6	0	0	0
SOWAHC	65124	hgsc.bcm.edu	37	2	110372192	110372192	+	Silent	SNP	A	A	G	rs6594048		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_023016	exon1	c.A126G	p.L42L	CGCCCTAGGCGGC	.	5	5	0	0	A|0.029;G|0.971	1	0	1	0	0
LRP1B	53353	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	141298589	141298589	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	LRP1B-311	NM_018557	exon45	c.G7466T	p.C2489F	CAGGAACAATTCA	.	77	62	115	2	.	0	0	0	0	0
SP5	389058	hgsc.bcm.edu	37	2	171573185	171573185	+	Silent	SNP	G	G	T	rs1134626	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SP5-90	NM_001003845	exon2	c.G468T	p.P156P	GCTGCCGCCAGGC	.	10	10	0	0	G|0.766;T|0.234	1	0	1	0	0
UNC80	285175	broad.mit.edu	37	2	210683895	210683895	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	UNC80-90	NM_182587	exon12	c.C1872A	p.D624E	CACAGACTCCTGC	.	155	3	160	0	.	0	0	0	0	0
AGXT	189	hgsc.bcm.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	241812461	241812461	+	Missense_Mutation	SNP	G	G	A	rs34664134	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	AGXT-90	NM_000030	exon5	c.G590A	p.R197Q	TGGACCGGCAAGG	.	45	37	72	0	G|0.993;A|0.007	0	0	0	0	0
FAM182B	728882	ucsc.edu	37	20	25755562	25755562	+	RNA	SNP	A	A	C	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	.	.	.	.	GGGACCACTCCGG	.	67	8	19	0	.	0	0	0	0	0
DNTTIP1	116092	hgsc.bcm.edu	37	20	44420682	44420682	+	Silent	SNP	T	T	C	rs2664591	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	DNTTIP1-91	NM_052951	exon1	c.T39C	p.P13P	GGGACCTAGCGGG	.	10	6	0	0	T|0.311;C|0.689	5	5	0	0	0
RNF114	55905	bcgsc.ca	37	20	48562681	48562681	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	RNF114-91	NM_018683	exon4	c.C407T	p.P136L	ATGTTCCAAACCG	.	127	56	84	2	.	0	0	0	0	0
TMEM189	387521	hgsc.bcm.edu	37	20	48770159	48770159	+	Missense_Mutation	SNP	T	T	C	rs232733		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	TMEM189-22	NM_199129	exon1	c.A16G	p.N6D	GCCAGTTCTCGGC	.	7	7	0	0	C|0.999;T|0.001	12	0	12	0	0
COL9A3	1299	broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	61470085	61470085	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	COL9A3-514	NM_001853	exon31	c.C1836T	p.D612D	GCTGGACGGGCCT	.	325	13	205	0	.	20	17	3	0	0
RTEL1	51750	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	20	62303930	62303930	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	RTEL1-44	NM_032957	exon9	c.G793T	p.D265Y	AACATTGACCTGA	.	143	36	107	1	.	18	12	6	0	0
SLC5A3	6526	broad.mit.edu	37	21	35468284	35468284	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SLC5A3-92	NM_006933	exon2	c.G787T	p.G263X	TGGCCTGGATTCA	.	127	5	154	0	.	12	12	0	0	0
KRTAP10-4	386672	ucsc.edu	37	21	45993851	45993851	+	Silent	SNP	C	C	T	rs543299		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	KRTAP10-4-90	NM_198687	exon1	c.C216T	p.C72C	GACCTGCGAGCCC	.	26	16	14	2	C|1.000;|0.000	0	0	0	0	0
PCNT	5116	ucsc.edu	37	21	47848459	47848459	+	Missense_Mutation	SNP	G	G	A	rs2839256	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PCNT-141	NM_006031	exon35	c.G7645A	p.A2549T	ACAAGCGCAGAGG	.	44	5	21	0	A|0.200;C|0.007	5	5	0	0	0
ZDHHC8	29801	bcgsc.ca	37	22	20131116	20131116	+	Missense_Mutation	SNP	G	G	A	rs80226867	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ZDHHC8-91	NM_001185024	exon10	c.G1963A	p.A655T	AGCAACGCCCCGG	.	47	39	8	0	G|0.962;A|0.038	11	0	11	0	0
PI4KA	5297	bcgsc.ca	37	22	21065645	21065645	+	Silent	SNP	A	A	G	rs444310	byfrequency;by2hit2allele	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PI4KA-454	NM_058004	exon51	c.T5907C	p.G1969G	GATATGACCCTTC	.	29	15	150	3	A|1.000;|0.000	58	3	55	0	0
UPK3A	7380	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	22	45691450	45691450	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	UPK3A-90	NM_006953	exon6	c.G714A	p.G238G	CATGGGGAGTTCT	.	55	45	73	0	.	0	0	0	0	0
CDCP1	64866	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	45135039	45135039	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CDCP1-117	NM_022842	exon6	c.C1357T	p.P453S	CCTTGGGCACCAG	.	146	69	94	0	.	0	0	0	0	0
FBXW12	285231	bcgsc.ca	37	3	48422235	48422235	+	Missense_Mutation	SNP	T	T	A	rs6784322	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	FBXW12-226	NM_207102	exon8	c.T818A	p.V273D	GCAGTGTTCCTCT	.	242	8	172	0	T|0.600;A|0.400	0	0	0	0	0
GPX1	2876	broad.mit.edu	37	3	49395674	49395679	+	In_Frame_Del	DEL	GCCGCC	GCCGCC	-	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	GPX1-68	.	.	.	.	GACTGGGCCGCCG	.	56	14	13	0	.	0	0	0	0	0
CNTN3	5067	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	74316498	74316498	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CNTN3-137	NM_020872	exon20	c.G2736T	p.W912C	GGCATTCCAAACA	.	137	23	94	0	.	0	0	0	0	0
PARP14	54625	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	122418659	122418659	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PARP14-525	NM_017554	exon6	c.G1258A	p.D420N	AAAGATGACAGGA	.	176	28	88	0	.	4	3	1	0	0
SEMA5B	54437	hgsc.bcm.edu	37	3	122631896	122631896	+	Missense_Mutation	SNP	A	A	T	rs2276782	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SEMA5B-157	NM_001256347	exon18	c.T2681A	p.V894D	AGGAGGACCTCCA	.	11	11	0	0	T|0.412;A|0.588	0	0	0	0	0
CLDN1	9076	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	190030751	190030751	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CLDN1-91	NM_021101	exon2	c.G298A	p.V100I	TGCCAACGGTGGC	.	235	44	176	0	.	181	160	21	0	0
DSPP	1834	bcgsc.ca	37	4	88536999	88536999	+	Missense_Mutation	SNP	A	A	G	rs202222170		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	DSPP-90	NM_014208	exon5	c.A3185G	p.D1062G	GCAGTGACAGCAG	.	276	16	354	0	.	0	0	0	0	0
SMAD1	4086	broad.mit.edu	37	4	146435774	146435774	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SMAD1-415	NM_005900	exon2	c.G9A	p.V3V	GAATGTGACAAGT	.	121	5	154	0	.	9	9	0	0	0
FAT1	2195	broad.mit.edu	37	4	187522507	187522507	+	Missense_Mutation	SNP	C	C	G	rs202035728		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	FAT1-34	NM_005245	exon21	c.G11556C	p.E3852D	TTTCATCTCTAAT	.	97	4	110	0	.	25	25	0	0	0
PAPD7	11044	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	6753081	6753081	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PAPD7-69	NM_001171805	exon12	c.C1365T	p.H455H	CGTCCACCACATG	.	99	81	110	0	.	19	1	18	0	0
ADCY2	108	bcgsc.ca	37	5	7520881	7520881	+	Missense_Mutation	SNP	G	G	T	rs13166360	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	ADCY2-97	NM_020546	exon3	c.G439T	p.V147L	TTCGTGGTGTACA	.	88	6	148	0	G|0.850;T|0.150	1	1	0	0	0
PCDHGA4	56111	broad.mit.edu	37	5	140736327	140736327	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_018917	exon1	c.C1560T	p.F520F	CTCCTTCGACTAT	.	110	4	114	0	.	8	8	0	0	0
RNF39	80352	hgsc.bcm.edu	37	6	30039364	30039364	+	Missense_Mutation	SNP	C	C	A	rs11753382		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	RNF39-226	NM_025236	exon4	c.G787T	p.G263C	TGGGGCCGTCAGG	.	13	12	1	0	C|0.862;A|0.138	2	0	2	0	0
NFKBIE	4794	hgsc.bcm.edu	37	6	44233372	44233372	+	Silent	SNP	G	G	A	rs189481001	by1000genomes	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	NFKBIE-135	NM_004556	exon1	c.C129T	p.G43G	GGCCCCGCCCCCT	.	7	7	1	0	G|0.995;A|0.005	0	0	0	0	0
TRAM2	9697	hgsc.bcm.edu	37	6	52380882	52380882	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	TRAM2-90	NM_012288	exon4	c.C333A	p.H111Q	CTTGCTGTGTTTG	.	80	4	96	0	.	11	11	0	0	0
COL21A1	81578	bcgsc.ca	37	6	56044578	56044578	+	Silent	SNP	T	T	C	rs2038149	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	COL21A1-24	NM_030820	exon3	c.A438G	p.K146K	TTGGGATTTGCCA	.	217	7	270	1	T|0.330;C|0.670	0	0	0	0	0
EEF1A1	1915	bcgsc.ca	37	6	74227973	74227973	+	Missense_Mutation	SNP	G	G	T	rs190893068		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	EEF1A1-226	NM_001402	exon7	c.C1044A	p.N348K	TGGATGGTTCAGG	.	233	14	249	5	G|0.999;T|0.001	16393	16376	8	5	4
POU3F2	5454	hgsc.bcm.edu	37	6	99283376	99283376	+	Silent	SNP	T	T	G	rs195860		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	POU3F2-90	NM_005604	exon1	c.T627G	p.G209G	GGCCGGTCTGCAC	.	7	7	0	0	T|0.089;G|0.911	0	0	0	0	0
HIVEP2	3097	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	143095218	143095218	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	HIVEP2-95	NM_006734	exon5	c.A658G	p.I220V	AAGGTATACATGG	.	118	82	139	0	.	1	0	1	0	0
SASH1	23328	bcgsc.ca	37	6	148792617	148792617	+	Silent	SNP	A	A	G	rs1883625	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SASH1-90	NM_015278	exon6	c.A492G	p.G164G	GAAAGGAATAATG	.	246	7	257	1	A|0.811;G|0.189	5	5	0	0	0
PION	54103	broad.mit.edu	37	7	77011934	77011934	+	Silent	SNP	A	A	G	rs112297229	alternate_allele	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PION-514	NM_017439	exon7	c.T483C	p.H161H	AAGAGGATGACTT	.	121	4	96	1	A|0.999;T|0.001	4	4	0	0	0
SEMA3E	9723	broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	83032010	83032010	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SEMA3E-93	NM_012431	exon10	c.G1081A	p.E361K	GTCCTTCCTTATG	.	169	25	117	1	.	0	0	0	0	0
GAL3ST4	79690	broad.mit.edu	37	7	99757680	99757680	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	GAL3ST4-47	NM_024637	exon4	c.C1332A	p.S444R	TTGGGGGCTCAAT	.	123	10	116	1	.	0	0	0	0	0
SPDYE3	441272	bcgsc.ca	37	7	99917416	99917416	+	Silent	SNP	G	G	A	rs112622797	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SPDYE3-22	NM_001004351	exon9	c.G1575A	p.P525P	TTCCCCGGAGGAG	.	113	7	75	1	G|0.905;A|0.095	32	21	11	0	0
RELN	5649	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	103276868	103276868	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	RELN-574	NM_173054	exon18	c.C2117T	p.T706I	GGGAATGTCTGGG	.	276	45	219	0	.	0	0	0	0	0
PODXL	5420	hgsc.bcm.edu	37	7	131241055	131241055	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PODXL-136	NM_001018111	exon1	c.T64C	p.S22P	GCGACGACGGCAG	.	21	5	0	0	.	10	10	0	0	0
DLGAP2	9228	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	1645390	1645390	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	DLGAP2-22	NM_004745	exon11	c.C2634T	p.D878D	TGAGGACGTCAGC	.	107	92	152	0	.	0	0	0	0	0
BHLHE22	27319	bcgsc.ca	37	8	65493429	65493429	+	Missense_Mutation	SNP	T	T	G	rs7016250	byfrequency	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	BHLHE22-90	NM_152414	exon1	c.T82G	p.S28A	TCCACCTCCAAGC	.	26	26	6	0	T|0.528;G|0.472	0	0	0	0	0
SPATA31D1	389763	broad.mit.edu;bcgsc.ca	37	9	84605762	84605762	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_001001670	exon4	c.C377T	p.P126L	TATGCCCAGACCC	.	88	4	139	0	.	0	0	0	0	0
FAM9A	171482	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	8763159	8763159	+	Missense_Mutation	SNP	T	T	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	FAM9A-130	NM_174951	exon7	c.A791T	p.E264V	TCTTCCTCTTCTT	.	48	7	84	0	.	0	0	0	0	0
SRPX	8406	broad.mit.edu	37	X	38079976	38079978	+	In_Frame_Del	DEL	GCA	GCA	-	rs35523939	alternate_allele	TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	SRPX-130	NM_001170751	exon1	c.68_70del	p.23_24del	GGACGCGCAGCAG	.	25	7	9	0	-|1.000;|0.000	0	0	0	0	0
BCOR	54880	broad.mit.edu;bcgsc.ca	37	X	39913284	39913284	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	BCOR-229	NM_001123385	exon14	c.G4831T	p.E1611X	CACTTTCATCATC	.	125	11	158	1	.	0	0	0	0	0
NUDT10	170685	broad.mit.edu	37	X	51076024	51076024	+	Silent	SNP	G	G	A	rs2801626		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	NUDT10-90	NM_153183	exon2	c.G207A	p.E69E	CGAAGAGGCGGGA	.	194	4	180	1	.	1	0	1	0	0
TGIF2LX	90316	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	89177681	89177681	+	Silent	SNP	C	C	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	TGIF2LX-92	NM_138960	exon2	c.C597A	p.S199S	CACATCCCCGTCT	.	348	132	354	0	.	0	0	0	0	0
TENM1	10178	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	123787622	123787622	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	.	NM_001163278	exon7	c.G1180T	p.G394X	CCCGTCCCTTCTG	.	74	33	111	0	.	0	0	0	0	0
FLNA	2316	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	153577797	153577797	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	FLNA-599	NM_001110556	exon47	c.G7689T	p.K2563N	CAGGCCCTTGGCC	.	102	39	129	1	.	102	102	0	0	0
CELSR2	1952	broad.mit.edu	37	1	109792735	109792736	+	In_Frame_Ins	INS	-	-	CGC	rs144034706		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CELSR2-526	NM_001408	exon1	c.34_35insCGC	p.T12delinsTP	CTCCCAACGCCGC	.	9	7	4	0	-|0.389;CGC|0.611	0	0	0	0	0
KRT2	3849	hgsc.bcm.edu	37	12	53045640	53045641	+	In_Frame_Ins	INS	-	-	AGCCGCTGCCGCCTCCAA	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	KRT2-92	NM_000423	exon1	c.287_288insTTGGAGGCGGCAGCGGCT	p.F96delinsFGGGSGF	CCTCCAAAACCAC	.	161	54	76	0	.	0	0	0	0	0
CTNNB1	1499	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	41266091	41266092	+	Nonsense_Mutation	INS	-	-	A	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CTNNB1-24361	NM_001098210	exon3	c.88_89insA	p.Y30_L31delinsX	CAGTCTTACCTGG	.	258	119	170	0	.	0	0	0	0	0
TBP	6908	broad.mit.edu	37	6	170871013	170871014	+	In_Frame_Ins	INS	-	-	CAG	rs201732168		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	TBP-91	NM_003194	exon3	c.189_190insCAG	p.Q63delinsQQ	ACAACAACAGCAG	.	38	19	54	0	-|0.138;CAG|0.862	0	0	0	0	0
PODXL	5420	hgsc.bcm.edu	37	7	131241029	131241030	+	In_Frame_Ins	INS	-	-	GGCGAC	rs11277659		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	PODXL-136	NM_005397	exon1	c.90_91insGTCGCC	p.P30delinsPSP	CTGGGAGGGCGAC	.	18	0	1	0	.	0	0	0	0	0
CYP4A22	284541	bcgsc.ca	37	1	47610300	47610301	+	Nonsense_Mutation	DNP	AC	AC	TA	novel		TCGA-OR-A5J2-01A-11D-A29I-10	TCGA-OR-A5J2-10A-01D-A29L-10	AC	AC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	d97c6076-7e4f-4dbe-85de-12bc0d84d8e8	367617cb-2dce-4769-bd48-49d49dd3d93a	.	CYP4A22-139	NM_001010969	exon8	c.C977A	p.T326*	ACACCACAGCCAG	.	440	0	548	0	.	0	0	0	0	0