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
FAM46B	115572	hgsc.bcm.edu	37	1	27339105	27339105	+	Silent	SNP	C	C	T	rs35810604	bycluster;byfrequency;by1000genomes	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FAM46B-90	NM_052943	exon1	c.G57A	p.G19G	AGCCGTCCCCACC	.	7	4	0	0	C|0.975;T|0.025	0	0	0	0	0
CLCA3P	9629	bcgsc.ca	37	1	87101375	87101375	+	RNA	SNP	C	C	G	rs2292830	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CLCA3P-90	.	.	.	.	GACCTACAAATCA	.	189	6	250	0	C|0.486;G|0.514	0	0	0	0	0
DENND2C	163259	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	115168233	115168233	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	DENND2C-229	NM_001256404	exon4	c.G373C	p.E125Q	AGCTTTCAATTTC	.	33	14	100	0	.	0	0	0	0	0
ANKRD34A	284615	hgsc.bcm.edu;bcgsc.ca	37	1	145474257	145474258	+	Frame_Shift_Del	DEL	CT	CT	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	CT	CT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ANKRD34A-68	NM_001039888	exon4	c.929_930del	p.310_310del	GGGGTCCTCTCTC	.	76	27	107	1	.	0	0	0	0	0
HRNR	388697	broad.mit.edu;bcgsc.ca	37	1	152188235	152188235	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	HRNR-93	NM_001009931	exon3	c.G5870A	p.G1957D	CCAGAACCAGACC	.	2930	70	2699	1	.	0	0	0	0	0
RRNAD1	51093	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	156703977	156703979	+	In_Frame_Del	DEL	CTC	CTC	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	CTC	CTC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	RRNAD1-90	NM_015997	exon6	c.813_815del	p.271_272del	ACACTTCTCCTGC	.	106	31	156	0	.	0	0	0	0	0
PEAR1	375033	broad.mit.edu;bcgsc.ca;mdanderson.org	37	1	156878718	156878718	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PEAR1-71	NM_001080471	exon11	c.G1301A	p.C434Y	CTCACTGTGCTAG	.	84	30	89	0	.	0	0	0	0	0
TOR3A	64222	hgsc.bcm.edu	37	1	179051300	179051300	+	Missense_Mutation	SNP	T	T	C	rs2296377	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TOR3A-90	NM_022371	exon1	c.T37C	p.F13L	CTCTTTTTCCTGC	.	7	4	2	0	T|0.229;C|0.771	6	2	4	0	0
CACNA1E	777	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	181767904	181767904	+	Silent	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CACNA1E-95	NM_001205293	exon48	c.G6876A	p.G2292G	GCCTGGGCCAGGC	.	55	24	26	0	.	0	0	0	0	0
RASSF5	83593	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	206730911	206730911	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	RASSF5-660	NM_182665	exon1	c.G10T	p.D4Y	ACCGTGGACAGCA	.	112	39	136	0	.	4	4	0	0	0
PARP1	142	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	226566961	226566961	+	Missense_Mutation	SNP	C	C	T	rs200485374		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PARP1-727	NM_001618	exon12	c.G1627A	p.A543T	CATGCGCAGAGTG	.	303	69	234	0	C|0.999;T|0.000	96	75	21	0	0
JMJD4	65094	hgsc.bcm.edu	37	1	227923081	227923081	+	Missense_Mutation	SNP	G	G	A	rs7419238		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	JMJD4-226	NM_023007	exon1	c.C32T	p.A11V	TGCCCCGCCAGCG	.	9	9	0	0	G|0.002;A|0.998	2	0	2	0	0
OBSCN	84033	hgsc.bcm.edu	37	1	228504670	228504670	+	Missense_Mutation	SNP	C	C	T	rs11810627	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	OBSCN-403	NM_001271223	exon62	c.C16417T	p.R5473W	TCTGCGCGGCTCA	.	31	31	0	0	C|0.643;T|0.357	0	0	0	0	0
OR2T2	401992	broad.mit.edu	37	1	248616705	248616711	+	Frame_Shift_Del	DEL	TGCTGCG	TGCTGCG	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	OR2T2-23	NM_001004136	exon1	c.607_613del	p.203_205del	TATGCCTGCTGCG	.	665	7	497	0	.	0	0	0	0	0
ANKRD16	54522	hgsc.bcm.edu	37	10	5931230	5931230	+	Missense_Mutation	SNP	C	C	T	rs3750659	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ANKRD16-90	NM_001009943	exon1	c.G88A	p.G30R	AGCCCCCGGCCGC	.	8	7	0	0	C|0.938;T|0.062	1	0	1	0	0
CDH23	64072	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	73571772	73571772	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CDH23-563	NM_022124	exon64	c.G9380A	p.G3127E	TTGATGGGTGAGT	.	292	63	224	0	.	0	0	0	0	0
HECTD2	143279	hgsc.bcm.edu	37	10	93170250	93170250	+	Missense_Mutation	SNP	C	C	G	rs7081569	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	HECTD2-658	NM_182765	exon1	c.C55G	p.P19A	GCGGCGCCCGCGC	.	6	6	0	0	C|0.154;G|0.846	2	0	2	0	0
TBC1D12	23232	hgsc.bcm.edu	37	10	96163039	96163039	+	Silent	SNP	C	C	G	rs2477534	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TBC1D12-68	NM_015188	exon1	c.C669G	p.P223P	CAGCCCCGCCAGC	.	35	35	0	0	C|0.339;G|0.661	1	0	1	0	0
TAF5	6877	hgsc.bcm.edu	37	10	105128134	105128134	+	Missense_Mutation	SNP	T	T	G	rs10883859	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TAF5-92	NM_006951	exon1	c.T388G	p.S130A	GCGGGCTCCGGAG	.	15	9	0	0	T|0.623;G|0.377	1	0	1	0	0
ZDHHC6	64429	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	114193036	114193036	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZDHHC6-90	NM_022494	exon8	c.G907A	p.E303K	ACTGTTCTATCTG	.	21	7	22	0	.	5	5	0	0	0
ENO4	387712	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	10	118639436	118639436	+	Silent	SNP	A	A	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ENO4-69	NM_001242699	exon13	c.A1662C	p.R554R	TGAACGAGTGACT	.	254	72	205	1	.	1	1	0	0	0
FANK1	92565	hgsc.bcm.edu	37	10	127585212	127585212	+	Missense_Mutation	SNP	A	A	T	rs145156460		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FANK1-91	NM_145235	exon1	c.A1T	p.M1L	CCGACCATGGAGC	.	179	10	23	0	.	0	0	0	0	0
KRTAP5-5	439915	broad.mit.edu;bcgsc.ca	37	11	1651116	1651127	+	In_Frame_Del	DEL	GGCCGTGGCTCC	GGCCGTGGCTCC	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KRTAP5-5-23	NM_001001480	exon1	c.46_57del	p.16_19del	TGTGGAGGCCGTG	.	288	7	152	0	.	0	0	0	0	0
SYT8	90019	hgsc.bcm.edu	37	11	1858572	1858572	+	Missense_Mutation	SNP	C	C	T	rs2292474	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SYT8-91	NM_138567	exon9	c.C1117T	p.R373W	GCCCAGCGGCACC	.	14	9	0	0	C|0.602;T|0.398	0	0	0	0	0
OR51F1	256892	bcgsc.ca	37	11	4790948	4790948	+	Missense_Mutation	SNP	C	C	A	rs11033800	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	OR51F1-70	NM_001004752	exon1	c.G200T	p.R67M	GATAGCCTGAAGA	.	147	6	159	1	C|0.707;A|0.293	0	0	0	0	0
OR51F1	256892	bcgsc.ca	37	11	4790951	4790951	+	Missense_Mutation	SNP	A	A	G	rs11033801	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	OR51F1-70	NM_001004752	exon1	c.T197C	p.F66S	AGCCTGAAGAGGA	.	146	6	155	2	A|0.702;G|0.298	0	0	0	0	0
AGBL2	79841	broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	47712028	47712028	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	AGBL2-92	NM_024783	exon10	c.G1231C	p.A411P	TGTTTGCCACTGA	.	157	20	207	1	.	0	0	0	0	0
OR5M11	219487	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	11	56310464	56310464	+	Silent	SNP	G	G	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_001005245	exon1	c.C270A	p.T90T	GGAAATGGTCTTC	.	153	44	203	0	.	0	0	0	0	0
LRRC10B	390205	hgsc.bcm.edu	37	11	61277031	61277031	+	Silent	SNP	C	C	T	rs1139011	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_001145077	exon1	c.C561T	p.L187L	CATCCTCGACCTC	.	16	14	0	0	C|0.816;T|0.184	0	0	0	0	0
CST6	1474	hgsc.bcm.edu	37	11	65779590	65779590	+	Silent	SNP	C	C	T	rs1131544		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CST6-523	NM_001323	exon1	c.C75T	p.D25D	ACGCGACGCCCGG	.	11	11	1	0	C|0.921;T|0.079	0	0	0	0	0
GAL3ST3	89792	hgsc.bcm.edu	37	11	65810209	65810209	+	Silent	SNP	C	C	T	rs61895584	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	GAL3ST3-91	NM_033036	exon3	c.G1065A	p.P355P	CTGCCACGGCTGC	.	9	9	0	0	C|0.233;T|0.767	0	0	0	0	0
PACS1	55690	broad.mit.edu	37	11	65988664	65988664	+	Silent	SNP	G	G	A	rs149576765		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PACS1-74	NM_018026	exon10	c.G1239A	p.T413T	CCAGACGGAGATT	.	360	7	356	1	G|1.000;A|0.000	15	15	0	0	0
FAM86C1	55199	hgsc.bcm.edu	37	11	71498671	71498671	+	Missense_Mutation	SNP	G	G	C	rs12283346	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FAM86C1-90	NM_152563	exon1	c.G89C	p.R30P	CCTTCCGCTGGCA	.	21	6	1	0	G|0.601;C|0.399	0	0	0	0	0
B3GNT6	192134	hgsc.bcm.edu	37	11	76751542	76751542	+	Splice_Site	DEL	T	T	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_138706	exon2	c.946+1T>-	.	TGTGTCTTGGAGC	.	11	10	0	0	.	0	0	0	0	0
KIAA1731	85459	broad.mit.edu;ucsc.edu	37	11	93462779	93462779	+	Splice_Site	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KIAA1731-22	NM_033395	exon27	c.7400-1G>A	.	CCAGCAGAAACCC	.	13	3	22	0	.	2	0	2	0	0
ATM	472	broad.mit.edu	37	11	108124536	108124540	+	Splice_Site	DEL	TGAAG	TGAAG	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ATM-3419	.	.	.	.	CTTTCTTGAAGTG	.	13	5	21	0	.	0	0	0	0	0
CADM1	23705	hgsc.bcm.edu	37	11	115375100	115375100	+	Missense_Mutation	SNP	C	C	G	rs112835318		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CADM1-92	NM_014333	exon1	c.G13C	p.V5L	GCAGCACTACACT	.	21	17	4	0	C|0.978;G|0.022	63	21	42	0	0
NECAP1	25977	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	8242868	8242868	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	NECAP1-91	NM_015509	exon3	c.T274G	p.F92V	CGCTACTTTGTAA	.	260	75	203	0	.	52	44	8	0	0
GPR19	2842	broad.mit.edu;bcgsc.ca	37	12	12815088	12815088	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	GPR19-91	NM_006143	exon4	c.A295G	p.T99A	TGGTGGTAGACTG	.	376	17	271	0	.	1	1	0	0	0
PIK3C2G	5288	broad.mit.edu	37	12	18641552	18641552	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PIK3C2G-1312	NM_004570	exon18	c.C2551T	p.H851Y	AGTGACCATCAAA	.	38	5	38	0	.	0	0	0	0	0
XPOT	11260	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	12	64813853	64813853	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	XPOT-652	NM_007235	exon7	c.G493A	p.A165T	TAGGAGGCTCGTA	.	175	19	24	0	.	0	0	0	0	0
PTPN11	5781	bcgsc.ca	37	12	112940034	112940034	+	Silent	SNP	T	T	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PTPN11-7239	NM_002834	exon14	c.T1686C	p.P562P	CCCGCCTTGTACT	.	204	28	171	1	.	29	29	0	0	0
GCN1L1	10985	broad.mit.edu	37	12	120595802	120595804	+	In_Frame_Del	DEL	AGG	AGG	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	GCN1L1-94	NM_006836	exon26	c.2936_2938del	p.979_980del	AGACTAAGGAGAA	.	174	9	192	0	.	0	0	0	0	0
MEDAG	84935	hgsc.bcm.edu	37	13	31480827	31480827	+	Missense_Mutation	SNP	A	A	G	rs9531945	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_032849	exon1	c.A175G	p.R59G	GTGGCCAGGCCCG	.	7	7	0	0	A|0.219;G|0.781	0	0	0	0	0
ING1	3621	hgsc.bcm.edu	37	13	111368316	111368316	+	Silent	SNP	C	C	T	rs9555726	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ING1-515	NM_005537	exon1	c.C526T	p.L176L	GCATCTCTGCTGA	.	5	4	0	0	C|0.372;T|0.628	7	5	2	0	0
APEX1	328	broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	20925557	20925557	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	APEX1-661	NM_080648	exon5	c.G847C	p.D283H	CGCCTTGATTACT	.	219	103	163	1	.	400	213	186	0	1
AJUBA	84962	broad.mit.edu	37	14	23451230	23451230	+	Silent	SNP	C	C	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_032876	exon1	c.G246T	p.A82A	GCGCGGCGCCTCA	.	58	6	19	0	.	0	0	0	0	0
DNAAF2	55172	hgsc.bcm.edu	37	14	50100683	50100683	+	Silent	SNP	C	C	G	rs2985686	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_018139	exon1	c.G1185C	p.A395A	GTCCTCCGCGCGA	.	5	4	0	0	C|0.569;G|0.431	1	0	1	0	0
KIAA0586	9786	hgsc.bcm.edu	37	14	58949383	58949383	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KIAA0586-23	NM_001244189	exon23	c.G3256T	p.A1086S	CCTGTTGCTACAG	.	68	4	79	0	.	3	3	0	0	0
COQ6	51004	bcgsc.ca	37	14	74424938	74424938	+	Silent	SNP	T	T	C	rs3180946	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	COQ6-90	NM_182476	exon5	c.T570C	p.H190H	GGTTCATATTACC	.	138	5	175	0	T|0.737;C|0.263	13	12	1	0	0
STON2	85439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	14	81743692	81743692	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	STON2-95	NM_001256430	exon6	c.G1963C	p.V655L	GGAAAACATCCTC	.	227	96	349	0	.	1	1	0	0	0
CKB	1152	hgsc.bcm.edu	37	14	103988180	103988180	+	Silent	SNP	G	G	T	rs1136165	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CKB-115	NM_001823	exon4	c.C456A	p.R152R	GATGGCGCGGCGC	.	4	4	0	0	G|0.327;T|0.673	56	0	56	0	0
KIF26A	26153	hgsc.bcm.edu	37	14	104644099	104644099	+	Silent	SNP	T	T	C	rs2497297	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KIF26A-24	NM_015656	exon12	c.T4974C	p.S1658S	CAGCAGTGGCTAT	.	7	7	0	0	T|0.603;C|0.397	1	0	1	0	0
MRPS34	65993	hgsc.bcm.edu	37	16	1823054	1823054	+	Missense_Mutation	SNP	C	C	G	rs11552432		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	MRPS34-92	NM_023936	exon1	c.G67C	p.E23Q	GTTGCTCCCGCAG	.	24	13	3	0	C|0.014;G|0.986	5	0	5	0	0
NTN3	4917	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	2523112	2523112	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	NTN3-90	NM_006181	exon3	c.G1244A	p.R415H	AAAGCCGCTCCCC	.	119	27	97	0	.	0	0	0	0	0
SCNN1B	6338	ucsc.edu;bcgsc.ca	37	16	23388659	23388659	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SCNN1B-157	NM_000336	exon10	c.G1356T	p.Q452H	CACCCAGTACAAG	.	39	4	73	1	.	0	0	0	0	0
ZNF423	23090	bcgsc.ca	37	16	49672520	49672520	+	Silent	SNP	A	A	G	rs3803665	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZNF423-228	NM_015069	exon4	c.T543C	p.R181R	CCGGTCACGGCTC	.	135	5	102	0	A|0.440;G|0.560	0	0	0	0	0
IRX3	79191	hgsc.bcm.edu	37	16	54318528	54318528	+	Missense_Mutation	SNP	A	A	G	rs1450355		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	IRX3-90	NM_024336	exon2	c.T1265C	p.L422P	GGGTGCAGGCGGG	.	4	4	0	0	T|0.035;G|0.004	0	0	0	0	0
NDRG4	65009	bcgsc.ca	37	16	58545426	58545426	+	Silent	SNP	A	A	G	rs42945	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	NDRG4-91	NM_001130487	exon16	c.A1122G	p.S374S	CCACTCAGAGAGC	.	269	8	190	2	A|0.274;G|0.726	14	14	0	0	0
TSNAXIP1	55815	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	16	67859153	67859153	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TSNAXIP1-90	NM_018430	exon7	c.C630G	p.D210E	GGAGGACATGTCA	.	129	44	164	0	.	0	0	0	0	0
ZNF23	7571	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	71482631	71482631	+	Missense_Mutation	SNP	A	A	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZNF23-90	NM_145911	exon6	c.T1297A	p.S433T	ATTGGGAGTTACA	.	33	7	39	0	.	5	4	1	0	0
ADAD2	161931	hgsc.bcm.edu	37	16	84224967	84224967	+	Missense_Mutation	SNP	G	G	A	rs8044695	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ADAD2-68	NM_001145400	exon1	c.G131A	p.G44E	CCTGGGGGCCCGC	.	7	7	0	0	G|0.292;A|0.708	0	0	0	0	0
ATP2C2	9914	broad.mit.edu	37	16	84456017	84456017	+	Nonsense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ATP2C2-91	NM_014861	exon8	c.G646T	p.E216X	GTGGATGAATCCA	.	169	5	231	0	.	0	0	0	0	0
ZFPM1	161882	hgsc.bcm.edu	37	16	88599696	88599697	+	Frame_Shift_Del	DEL	GA	GA	-	rs67549438	alternate_allele	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	GA	GA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZFPM1-90	NM_153813	exon10	c.1330_1331del	p.444_444del	AGAGCGGAGCCTC	.	17	13	1	0	.	0	0	0	0	0
ZFPM1	161882	hgsc.bcm.edu	37	16	88599697	88599705	+	In_Frame_Del	DEL	AGCCTCTGG	AGCCTCTGG	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	AGCCTCTGG	AGCCTCTGG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZFPM1-90	NM_153813	exon10	c.1331_1339del	p.444_447del	GAGCGGAGCCTCT	.	16	0	1	0	.	0	0	0	0	0
ZFPM1	161882	hgsc.bcm.edu	37	16	88599701	88599701	+	Frame_Shift_Del	DEL	T	T	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZFPM1-90	NM_153813	exon10	c.1335delT	p.P445fs	GGAGCCTCTGGCC	.	14	10	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-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	TGG	TGG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZFPM1-90	NM_153813	exon10	c.1337_1339del	p.446_447del	AGCCTCTGGCCCA	.	13	10	0	0	.	0	0	0	0	0
RPL13	6137	hgsc.bcm.edu	37	16	89627671	89627671	+	Silent	SNP	C	C	T	rs174035	bycluster;byfrequency;by1000genomes	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	RPL13-90	NM_001243131	exon3	c.C141T	p.A47A	CATCGCCCCGCGC	.	12	12	0	0	C|0.846;T|0.154	1487	2	1479	1	5
PELP1	27043	bcgsc.ca	37	17	4576620	4576620	+	Silent	SNP	C	C	T	rs55677157	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PELP1-24	NM_014389	exon15	c.G1770A	p.P590P	AGGAGACGGGGCC	.	140	6	227	3	C|0.892;T|0.108	16	16	0	0	0
NUFIP2	57532	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	27614591	27614591	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	NUFIP2-138	NM_020772	exon2	c.G421C	p.A141P	TGTTGGCCTTTAC	.	142	53	78	0	.	10	6	4	0	0
NR1D1	9572	hgsc.bcm.edu;bcgsc.ca	37	17	38252715	38252716	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	AG	AG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	NR1D1-226	NM_021724	exon4	c.584_585del	p.195_195del	GCCCACAGAGAGA	.	191	86	178	1	.	0	0	0	0	0
KRTAP9-1	728318	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	17	39346567	39346567	+	Nonsense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_001190460	exon1	c.C429A	p.C143X	CACCTGCTGCAGG	.	205	46	146	0	.	0	0	0	0	0
KRT33A	3883	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	39505635	39505635	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KRT33A-90	NM_004138	exon2	c.G394T	p.D132Y	CATTGTCGATCTG	.	208	62	171	0	.	0	0	0	0	0
UBTF	7343	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	42288160	42288162	+	In_Frame_Del	DEL	CTT	CTT	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	CTT	CTT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	UBTF-90	NM_014233	exon13	c.1357_1359del	p.453_453del	CCTGACCTTCTTC	.	128	53	59	0	.	0	0	0	0	0
CBX4	8535	hgsc.bcm.edu;broad.mit.edu	37	17	77807927	77807927	+	Missense_Mutation	SNP	A	A	G	rs200965379		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CBX4-228	NM_003655	exon5	c.T1514C	p.V505A	GCCGCCACCGCCA	.	42	20	10	0	.	9	9	0	0	0
CARD14	79092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	78172210	78172210	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CARD14-231	NM_024110	exon13	c.G1671A	p.M557I	CCTCATGCGGCGG	.	93	32	46	0	.	0	0	0	0	0
SEH1L	81929	hgsc.bcm.edu	37	18	12955467	12955467	+	Silent	SNP	T	T	C	rs2015378		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SEH1L-90	NM_001013437	exon3	c.T168C	p.H56H	GACACATAGTGGA	.	99	5	68	0	.	0	0	0	0	0
IMPACT	55364	broad.mit.edu	37	18	22023012	22023012	+	Splice_Site	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	IMPACT-90	NM_018439	exon7	c.491-1G>A	.	TTTCTAGAAGTAG	.	34	6	48	0	.	0	0	0	0	0
DSC3	1825	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	18	28605791	28605791	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	DSC3-94	NM_024423	exon5	c.G565C	p.E189Q	CTCTTTCTATATA	.	138	8	178	0	.	0	0	0	0	0
SALL3	27164	hgsc.bcm.edu	37	18	76753768	76753768	+	Missense_Mutation	SNP	C	C	G	rs2447437	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SALL3-155	NM_171999	exon2	c.C1777G	p.L593V	CCGCCCCTCACTA	.	7	7	0	0	C|0.780;G|0.220	0	0	0	0	0
KISS1R	84634	hgsc.bcm.edu	37	19	917526	917526	+	Silent	SNP	A	A	G	rs10407968	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KISS1R-91	NM_032551	exon1	c.A24G	p.G8G	GTCCGGACCCAAC	.	9	7	0	0	A|0.821;G|0.179	0	0	0	0	0
ARID3A	1820	hgsc.bcm.edu	37	19	929678	929678	+	Silent	SNP	G	G	A	rs3826948		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ARID3A-90	NM_005224	exon2	c.G150A	p.E50E	GCCCGAGAGTGCC	.	4	4	0	0	T|0.495;C|0.504	2	0	2	0	0
ARID3A	1820	hgsc.bcm.edu	37	19	929753	929753	+	Silent	SNP	A	A	G	rs1799595		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ARID3A-90	NM_005224	exon2	c.A225G	p.P75P	ACACCCAGCCAGC	.	14	14	0	0	A|0.114;G|0.886	3	0	3	0	0
KLF16	83855	hgsc.bcm.edu	37	19	1854557	1854557	+	Silent	SNP	A	A	G	rs3746045	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KLF16-90	NM_031918	exon2	c.T660C	p.P220P	GGCACCAGGGCGC	.	26	11	0	0	A|0.591;G|0.409	39	28	11	0	0
UHRF1	29128	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	4950704	4950704	+	RNA	SNP	C	C	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	UHRF1-522	.	.	.	.	GCCGGTCAGGGTG	.	400	76	316	1	.	14	11	3	0	0
FUT6	2528	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	19	5832103	5832103	+	Missense_Mutation	SNP	C	C	T	rs140726017		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FUT6-90	NM_000150	exon3	c.G476A	p.R159H	TCGCTGCGGTAGG	.	373	160	282	0	C|1.000;T|0.000	0	0	0	0	0
ZNF653	115950	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	11598309	11598309	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZNF653-90	NM_138783	exon4	c.G969A	p.A323A	AGGGCCCGCAATG	.	172	36	65	0	.	16	16	0	0	0
MAP1S	55201	hgsc.bcm.edu	37	19	17837417	17837417	+	Silent	SNP	G	G	A	rs138676223		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	MAP1S-90	NM_018174	exon5	c.G1224A	p.T408T	GCGCACGCTGGCC	.	37	29	2	0	G|0.987;A|0.013	14	6	8	0	0
MAP1S	55201	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	17838767	17838767	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	MAP1S-90	NM_018174	exon5	c.C2574T	p.N858N	GGAGAACGTCAGC	.	134	36	31	0	.	37	31	6	0	0
ZNF737	100129842	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	20728340	20728340	+	Silent	SNP	A	A	G	rs187919890	by1000genomes	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZNF737-1	NM_001159293	exon4	c.T669C	p.H223H	TCCAGTATGAATT	.	44	17	34	0	A|0.999;G|0.000	2	2	0	0	0
LGI4	163175	hgsc.bcm.edu	37	19	35617513	35617513	+	Silent	SNP	G	G	C	rs77635806		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	LGI4-91	NM_139284	exon8	c.C960G	p.A320A	GAGCTCGGCGTCA	.	17	10	0	0	G|0.981;C|0.019	0	0	0	0	0
MLL4	8085	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	36211355	36211357	+	In_Frame_Del	DEL	AAG	AAG	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	AAG	AAG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	MLL4-697	NM_014727	exon3	c.1106_1108del	p.369_370del	AGAAGAAAGAAGA	.	120	29	128	0	.	0	0	0	0	0
RINL	126432	hgsc.bcm.edu	37	19	39360720	39360720	+	Missense_Mutation	SNP	G	G	A	rs8110393		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	RINL-91	NM_001195833	exon9	c.C1205T	p.P402L	GGGGCGGGGCTCT	.	15	15	1	0	G|0.349;A|0.651	0	0	0	0	0
ERCC2	2068	hgsc.bcm.edu	37	19	45867259	45867259	+	Missense_Mutation	SNP	C	C	T	rs1799793	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ERCC2-848	NM_000400	exon10	c.G934A	p.D312N	CTTCGTCGGGCAG	.	26	12	1	0	C|0.804;T|0.196	25	12	13	0	0
GPR4	2828	broad.mit.edu	37	19	46094763	46094763	+	Missense_Mutation	SNP	T	T	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	GPR4-92	NM_005282	exon2	c.A362C	p.H121P	AGTGGGTGGGCCA	.	135	52	69	12	.	5	4	1	0	0
PNMAL2	57469	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	46997582	46997582	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PNMAL2-1	NM_020709	exon1	c.A1141G	p.K381E	TGTCCTTGGACAT	.	69	16	66	0	.	8	5	3	0	0
GLTSCR2	29997	hgsc.bcm.edu	37	19	48258717	48258717	+	Missense_Mutation	SNP	A	A	G	rs1804994	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	GLTSCR2-514	NM_015710	exon9	c.A1166G	p.Q389R	GGCGGCAGAGGCG	.	10	10	0	0	A|0.308;G|0.692	34	0	34	0	0
IZUMO2	126123	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	50666247	50666247	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	IZUMO2-90	NM_152358	exon1	c.G205T	p.A69S	TCAGCGCGTAGTC	.	274	71	149	0	.	0	0	0	0	0
ZNF628	89887	hgsc.bcm.edu	37	19	55993260	55993260	+	Missense_Mutation	SNP	A	A	G	rs34864744		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZNF628-22	NM_033113	exon3	c.A700G	p.T234A	CCGGGTACCGCCT	.	10	9	0	0	A|0.270;G|0.730	0	0	0	0	0
CMPK2	129607	hgsc.bcm.edu	37	2	7005369	7005369	+	Silent	SNP	A	A	G	rs11678810		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CMPK2-68	NM_001256478	exon1	c.T459C	p.C153C	CTCCTGACAGGCG	.	11	11	0	0	A|0.003;G|0.997	1	0	1	0	0
FEZ2	9637	hgsc.bcm.edu	37	2	36825137	36825137	+	Missense_Mutation	SNP	G	G	A	rs1544655		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FEZ2-23	NM_001042548	exon1	c.C149T	p.P50L	CAGGCCGGGGCCG	.	7	7	0	0	T|0.817;C|0.180	19	0	19	0	0
TTC31	64427	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	74710496	74710496	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TTC31-90	NM_022492	exon2	c.A88C	p.K30Q	GCACCCAAACTTT	.	98	5	95	0	.	14	14	0	0	0
CD8B	926	hgsc.bcm.edu	37	2	87088964	87088964	+	Silent	SNP	A	A	G	rs62146888	byfrequency;by1000genomes	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CD8B-92	NM_004931	exon1	c.T25C	p.L9L	CGGCCAAGAGGAG	.	7	4	1	0	A|0.476;G|0.524	0	0	0	0	0
SNRNP200	23020	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	96965141	96965141	+	Frame_Shift_Del	DEL	C	C	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SNRNP200-162	NM_014014	exon6	c.655delG	p.E219fs	GAACCTCCCCGTA	.	173	32	158	0	.	0	0	0	0	0
SCN3A	6328	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	2	166032830	166032830	+	Silent	SNP	G	G	T	rs112118503	alternate_allele	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SCN3A-141	NM_001081676	exon3	c.C75A	p.I25I	TTTTTCGATAGCA	.	66	23	78	0	G|0.500;A|0.500	0	0	0	0	0
PDE11A	50940	bcgsc.ca	37	2	178762824	178762824	+	Silent	SNP	T	T	C	rs71423514	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PDE11A-93	NM_016953	exon4	c.A1263G	p.E421E	ACAGCGTTCACAT	.	57	4	73	0	T|0.895;C|0.105	0	0	0	0	0
TTN	7273	broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	179586707	179586707	+	Silent	SNP	A	A	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TTN-636	NM_001267550	exon78	c.T22683C	p.Y7561Y	GATTGTATAGTTT	.	233	77	245	1	.	0	0	0	0	0
FAM171B	165215	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	2	187626567	187626567	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FAM171B-141	NM_177454	exon8	c.A1498G	p.N500D	AACAACAATCTAT	.	74	21	87	0	.	2	2	0	0	0
COL5A2	1290	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	189963460	189963460	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	COL5A2-92	NM_000393	exon5	c.G395A	p.G132E	GCCGGTCCTGGAC	.	40	7	68	0	.	0	0	0	0	0
CST3	1471	hgsc.bcm.edu	37	20	23618488	23618488	+	Silent	SNP	G	G	A	rs1055084		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CST3-91	NM_000099	exon1	c.C12T	p.P4P	GCGCAGGGGCCCG	.	5	4	0	0	T|0.037;C|0.962	254	58	196	0	0
VSX1	30813	bcgsc.ca	37	20	25059546	25059546	+	Silent	SNP	T	T	C	rs12480307	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	VSX1-90	NM_014588	exon3	c.A546G	p.A182A	GCTGAATGCCTTC	.	183	6	128	0	T|0.715;C|0.285	0	0	0	0	0
OGFR	11054	hgsc.bcm.edu	37	20	61444569	61444569	+	Silent	SNP	A	A	G	rs3204348	byfrequency;by1000genomes	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	OGFR-68	NM_007346	exon7	c.A1602G	p.P534P	CGAGCCAGCCGAG	.	57	11	27	0	A|0.979;G|0.021	123	99	24	0	0
OGFR	11054	hgsc.bcm.edu	37	20	61444633	61444633	+	Missense_Mutation	SNP	G	G	A	rs75570150		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	OGFR-68	NM_007346	exon7	c.G1666A	p.E556K	CCAGCCGAGAGCC	.	44	12	6	0	.	92	92	0	0	0
OGFR	11054	hgsc.bcm.edu	37	20	61444637	61444637	+	Missense_Mutation	SNP	G	G	C	rs78981100		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	OGFR-68	NM_007346	exon7	c.G1670C	p.S557T	CCGAGAGCCCATC	.	42	10	4	0	.	89	89	0	0	0
CECR5	27440	hgsc.bcm.edu	37	22	17640022	17640022	+	Silent	SNP	G	G	C	rs11550530		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CECR5-514	NM_033070	exon1	c.C120G	p.P40P	CTGAGCGGGGCCC	.	21	7	0	0	.	0	0	0	0	0
SCARF2	91179	hgsc.bcm.edu	37	22	20780097	20780097	+	Silent	SNP	G	G	C	rs759609	bycluster;byfrequency;by1000genomes	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SCARF2-341	NM_153334	exon11	c.C2181G	p.R727R	CGGGGGGCGCGGC	.	4	4	0	0	G|0.826;C|0.174	0	0	0	0	0
CHEK2	11200	broad.mit.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs74751600		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CHEK2-1515	NM_001005735	exon12	c.A1246G	p.K416E	AAATCTTGGAGTG	.	205	14	196	2	.	25	25	0	0	0
SH3BP1	23616	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	22	38051288	38051288	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SH3BP1-90	NM_018957	exon18	c.C1703T	p.P568L	AGCGCCCGGCGCC	.	79	31	40	0	.	0	0	0	0	0
TRIOBP	11078	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	22	38122417	38122417	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TRIOBP-136	NM_001039141	exon7	c.G3854C	p.R1285T	CCCAGAGACAGCC	.	67	19	15	0	.	2	2	0	0	0
LMF2	91289	broad.mit.edu;bcgsc.ca	37	22	50946029	50946029	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	LMF2-153	NM_033200	exon1	c.C76T	p.L26F	TGTAGAGGGAAGC	.	172	6	175	0	.	37	34	3	0	0
CTNNB1	1499	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	3	41266134	41266136	+	In_Frame_Del	DEL	CTT	CTT	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	CTT	CTT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CTNNB1-24361	NM_001098209	exon3	c.131_133del	p.44_45del	CAGCTCCTTCTCT	.	162	51	210	0	.	0	0	0	0	0
NKTR	4820	hgsc.bcm.edu;broad.mit.edu	37	3	42679924	42679926	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	GAA	GAA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	NKTR-93	NM_005385	exon13	c.2728_2730del	p.910_910del	GACAAGGAAGAAG	.	190	11	186	0	.	0	0	0	0	0
QARS	5859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	49136628	49136628	+	Missense_Mutation	SNP	C	C	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	QARS-91	NM_005051	exon18	c.G1673C	p.R558P	ACATCACGCACAC	.	155	51	193	0	.	197	122	75	0	0
USP19	10869	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	49155468	49155468	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	USP19-663	NM_001199160	exon3	c.G210A	p.G70G	TGTGATCCCAGCT	.	54	22	60	0	.	8	7	1	0	0
LRIG1	26018	hgsc.bcm.edu	37	3	66550762	66550762	+	Missense_Mutation	SNP	G	G	C	rs1403626	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	LRIG1-230	NM_015541	exon1	c.C70G	p.L24V	GCAAAAGCAGCCA	.	5	5	0	0	G|0.252;C|0.748	0	0	0	0	0
OR5K3	403277	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	98110047	98110047	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	OR5K3-68	NM_001005516	exon1	c.G538A	p.D180N	TTCTGTGATGTTC	.	54	10	62	0	.	0	0	0	0	0
CCDC14	64770	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	3	123633689	123633689	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CCDC14-68	NM_022757	exon12	c.G2676A	p.A892A	TAATGCCGCAAGG	.	122	35	102	0	.	28	17	11	0	0
EFCC1	79825	hgsc.bcm.edu	37	3	128720487	128720487	+	Missense_Mutation	SNP	A	A	G	rs1871951	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_024768	exon1	c.A16G	p.T6A	GTCAGCACGGGCG	.	5	5	0	0	A|0.315;G|0.685	0	0	0	0	0
PLXND1	23129	hgsc.bcm.edu	37	3	129324982	129324982	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PLXND1-90	NM_015103	exon1	c.G501A	p.A167A	GGGCGGCGCGGCG	.	6	6	0	0	.	0	0	0	0	0
IDUA	3425	broad.mit.edu	37	4	996204	996204	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	IDUA-91	NM_000203	exon8	c.A1120C	p.T374P	AACAACACCCGCC	.	244	106	91	19	.	5	5	0	0	0
MSX1	4487	hgsc.bcm.edu	37	4	4861745	4861745	+	Missense_Mutation	SNP	C	C	G	rs36059701		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	MSX1-90	NM_002448	exon1	c.C119G	p.A40G	CCACGGCAGCCGC	.	7	7	0	0	C|0.867;G|0.133	3	2	1	0	0
FAM184B	27146	hgsc.bcm.edu	37	4	17643848	17643848	+	Missense_Mutation	SNP	G	G	A	rs2286771	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FAM184B-23	NM_015688	exon13	c.C2350T	p.R784W	CGCCCCGCTCCTG	.	15	12	0	0	G|0.440;A|0.560	1	0	1	0	0
GPR125	166647	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	22390318	22390319	+	Frame_Shift_Del	DEL	AA	AA	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	AA	AA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	GPR125-91	NM_145290	exon19	c.2975_2976del	p.992_992del	AGAATGAAAAGTG	.	71	17	80	0	.	0	0	0	0	0
KIAA1211	57482	bcgsc.ca	37	4	57190356	57190356	+	Silent	SNP	G	G	A	rs7695701	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KIAA1211-70	NM_020722	exon10	c.G3465A	p.R1155R	GAAGAGGCCCGAG	.	399	11	339	4	G|0.741;A|0.259	1	1	0	0	0
PCDH18	54510	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	138442524	138442524	+	Missense_Mutation	SNP	A	A	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PCDH18-185	NM_019035	exon4	c.T3067C	p.Y1023H	CAGAATAGGTGTC	.	134	66	214	0	.	3	3	0	0	0
FAM149A	25854	hgsc.bcm.edu	37	4	187077240	187077240	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FAM149A-90	NM_001006655	exon6	c.G470T	p.C157F	GTGACTGTGTCAA	.	80	4	125	0	.	5	5	0	0	0
FAT1	2195	bcgsc.ca	37	4	187522528	187522528	+	Silent	SNP	C	C	T	rs2289550	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FAT1-34	NM_005245	exon21	c.G11535A	p.T3845T	ATTTTCCGTCAGA	.	79	4	138	0	C|0.934;T|0.066	44	44	0	0	0
PLK2	10769	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	5	57755592	57755592	+	Silent	SNP	C	C	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PLK2-409	NM_006622	exon1	c.G195C	p.S65S	CGGCCCCGAGTGC	.	72	22	37	0	.	37	26	11	0	0
SOWAHA	134548	hgsc.bcm.edu	37	5	132149684	132149684	+	Missense_Mutation	SNP	G	G	C	rs40274	bycluster;byfrequency;by2hit2allele;byhapmap;by1000genomes	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_175873	exon1	c.G371C	p.R124P	TGGTCCGGGTGCC	.	8	8	0	0	G|0.980;C|0.020	0	0	0	0	0
HSPA4	3308	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	132406071	132406072	+	Frame_Shift_Del	DEL	AT	AT	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	AT	AT	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	HSPA4-226	NM_002154	exon4	c.312_313del	p.104_105del	GGTGACATATATG	.	93	26	68	0	.	0	0	0	0	0
PCDHA3	56145	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	5	140182806	140182806	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PCDHA3-98	NM_031497	exon1	c.C2024A	p.A675E	GCCAGGCACCCAA	.	254	85	101	2	.	0	0	0	0	0
PWWP2A	114825	hgsc.bcm.edu	37	5	159546013	159546013	+	Missense_Mutation	SNP	T	T	C	rs56806495	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PWWP2A-68	NM_052927	exon1	c.A383G	p.E128G	CGCTCCTCGGGAG	.	7	5	0	0	T|0.943;C|0.057	1	0	1	0	0
ECI2	10455	broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	4116248	4116248	+	Missense_Mutation	SNP	T	T	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ECI2-90	NM_206836	exon10	c.A1045G	p.K349E	CCTCTTTTGAAAT	.	171	49	152	2	.	552	418	134	0	0
PPP1R3G	648791	hgsc.bcm.edu	37	6	5086070	5086070	+	Silent	SNP	A	A	G	rs667752		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PPP1R3G-136	NM_001145115	exon1	c.A351G	p.A117A	GGACGCACAGCTC	.	21	21	0	0	A|0.006;G|0.994	8	0	8	0	0
PPP1R3G	648791	hgsc.bcm.edu	37	6	5086211	5086211	+	Silent	SNP	G	G	C	rs584962		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PPP1R3G-136	NM_001145115	exon1	c.G492C	p.L164L	GCGCCTGCGAAGC	.	7	7	0	0	G|0.000;C|1.000	8	0	8	0	0
RNF144B	255488	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	18459916	18459916	+	Silent	SNP	C	C	A	rs139497819		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	RNF144B-226	NM_182757	exon6	c.C615A	p.G205G	TGAAGGCTGCGCT	.	188	44	143	0	C|1.000;A|0.000	0	0	0	0	0
LY6G5C	80741	broad.mit.edu	37	6	31646904	31646904	+	Missense_Mutation	SNP	C	C	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	LY6G5C-90	NM_025262	exon2	c.G263T	p.S88I	ATGCAGCTGCTGC	.	256	7	182	1	.	0	0	0	0	0
NELFE	7936	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	31922199	31922199	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_002904	exon8	c.C763T	p.R255W	CTCGCCGTTCAGG	.	131	27	107	0	.	121	93	28	0	0
PKHD1	5314	broad.mit.edu	37	6	51720866	51720866	+	Missense_Mutation	SNP	G	G	T	rs78361537	byfrequency;alternate_allele	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PKHD1-603	NM_170724	exon49	c.C7736A	p.A2579E	GTATTCGCTCTAA	.	90	3	54	0	G|0.999;A|0.001	0	0	0	0	0
KHDC1L	100129128	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	73935030	73935032	+	In_Frame_Del	DEL	CTC	CTC	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	CTC	CTC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KHDC1L-1	NM_001126063	exon1	c.100_102del	p.34_34del	GATGAGCTCCTCC	.	120	35	110	0	.	0	0	0	0	0
KIAA1009	22832	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	84896081	84896083	+	In_Frame_Del	DEL	GAA	GAA	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	GAA	GAA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	KIAA1009-91	NM_014895	exon12	c.1368_1370del	p.456_457del	AATGATGAAGAAT	.	88	16	84	0	.	0	0	0	0	0
TMEM200A	114801	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	130762220	130762220	+	Missense_Mutation	SNP	G	G	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TMEM200A-23	NM_001258277	exon3	c.G653C	p.S218T	TTCGGAGCAGTTT	.	145	55	160	0	.	8	4	4	0	0
TAAR9	134860	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	132860125	132860125	+	RNA	SNP	A	A	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	.	.	.	.	ATAGAAAGTACAG	.	52	15	60	0	.	0	0	0	0	0
SERAC1	84947	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	158569912	158569912	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SERAC1-90	NM_032861	exon5	c.C340T	p.R114W	GATTCCGCAGTAT	.	116	28	62	0	.	8	8	0	0	0
TCP10	6953	broad.mit.edu;bcgsc.ca	37	6	167787940	167787940	+	Splice_Site	SNP	C	C	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TCP10-89	NM_004610	exon8	c.689-1G>T	.	TTCTGTCTAAAAA	.	1345	54	841	1	.	0	0	0	0	0
SUN1	23353	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	900013	900014	+	Frame_Shift_Del	DEL	AG	AG	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	AG	AG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SUN1-90	NM_001130965	exon14	c.1773_1774del	p.591_592del	AATAACAGAGGCG	.	122	38	142	0	.	0	0	0	0	0
MICALL2	79778	hgsc.bcm.edu	37	7	1484572	1484572	+	Silent	SNP	A	A	G	rs10435184		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	MICALL2-90	NM_182924	exon6	c.T1134C	p.G378G	TCCCCCACCCTGG	.	5	5	0	0	A|0.009;G|0.991	8	0	8	0	0
RBAK	57786	broad.mit.edu	37	7	5104585	5104585	+	Missense_Mutation	SNP	G	G	A	rs149739845	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	RBAK-653	NM_001204456	exon6	c.G1498A	p.D500N	CTCACCGACCATC	.	91	4	86	0	G|0.999;A|0.001	5	5	0	0	0
TNRC18	84629	bcgsc.ca	37	7	5347914	5347914	+	Silent	SNP	G	G	A	rs11554710	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TNRC18-46	NM_001080495	exon30	c.C8730T	p.D2910D	ATTTTCGTCCACA	.	305	11	307	0	G|0.862;A|0.138	40	40	0	0	0
USP42	84132	bcgsc.ca	37	7	6189780	6189780	+	Silent	SNP	T	T	C	rs3764814	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	USP42-659	NM_032172	exon13	c.T1953C	p.L651L	CGAGCTTCAAGAA	.	82	5	107	0	T|0.728;C|0.272	7	7	0	0	0
WIPF3	644150	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	29923752	29923752	+	Silent	SNP	G	G	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	WIPF3-69	NM_001080529	exon5	c.G642C	p.V214V	CCCGGTGGTTGCA	.	44	11	27	0	.	1	1	0	0	0
GARS	2617	hgsc.bcm.edu	37	7	30634661	30634661	+	Missense_Mutation	SNP	C	C	G	rs1049402	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	GARS-91	NM_002047	exon1	c.C124G	p.P42A	TCCTGCCCCCCGA	.	12	12	0	0	C|0.329;G|0.671	14	0	14	0	0
AVL9	23080	bcgsc.ca	37	7	32598630	32598630	+	Missense_Mutation	SNP	T	T	A	rs2290213	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	AVL9-90	NM_015060	exon10	c.T769A	p.C257S	AACCCATGTGCAG	.	106	5	149	0	A|0.150;C|0.000;T|0.850	14	14	0	0	0
NT5C3A	0	bcgsc.ca	37	7	33060946	33060946	+	Silent	SNP	A	A	G	rs3750117	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_001002010	exon5	c.T393C	p.Y131Y	AGCGTAATATTTT	.	392	9	424	4	A|0.300;G|0.700	21	21	0	0	0
URGCP	55665	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	43916339	43916340	+	Frame_Shift_Del	DEL	TC	TC	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	TC	TC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	URGCP-94	NM_001077663	exon6	c.2722_2723del	p.908_908del	ATGTTTTCGAGTA	.	173	54	176	0	.	0	0	0	0	0
LRRD1	401387	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	91793979	91793979	+	Nonsense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_001161528	exon1	c.C538T	p.Q180X	CCCCTTGAAATGT	.	38	16	58	0	.	0	0	0	0	0
EPHB4	2050	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	100416169	100416169	+	Silent	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	EPHB4-1446	NM_004444	exon7	c.G1395A	p.L465L	GTAGTCCAGCACA	.	60	23	60	0	.	16	11	5	0	0
UFSP1	402682	broad.mit.edu	37	7	100486576	100486576	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	UFSP1-22	NM_001015072	exon1	c.C317A	p.A106D	CCAGCAGCCTGTA	.	70	5	125	2	.	2	2	0	0	0
RBM33	155435	bcgsc.ca	37	7	155530954	155530954	+	Silent	SNP	T	T	C	rs2178428	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	RBM33-23	NM_053043	exon11	c.T1594C	p.L532L	CCAGCCTTGCAGC	.	137	7	224	2	T|0.708;C|0.292	1	1	0	0	0
DLC1	10395	hgsc.bcm.edu;broad.mit.edu	37	8	12943918	12943919	+	Frame_Shift_Del	DEL	CA	CA	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	CA	CA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	DLC1-657	NM_182643	exon17	c.4346_4347del	p.1449_1449del	GTGATCCACAGAG	.	175	16	108	0	.	0	0	0	0	0
OPRK1	4986	hgsc.bcm.edu	37	8	54163562	54163562	+	Silent	SNP	C	C	A	rs1051660	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	OPRK1-70	NM_000912	exon2	c.G36T	p.P12P	AGGGCCCGGCTCC	.	11	7	3	0	C|0.895;A|0.105	0	0	0	0	0
ANKRD46	157567	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	101540156	101540156	+	Silent	SNP	T	T	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ANKRD46-22	NM_001270378	exon4	c.A387G	p.E129E	CAAAGATTCCAGC	.	128	29	98	0	.	18	18	0	0	0
TMEM74	157753	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	8	109796810	109796810	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	TMEM74-228	NM_153015	exon2	c.C518T	p.S173F	TCTATAGACTTCC	.	256	42	180	0	.	0	0	0	0	0
SCRIB	23513	hgsc.bcm.edu	37	8	144874554	144874554	+	Silent	SNP	T	T	C	rs6991873		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SCRIB-228	NM_015356	exon32	c.A4350G	p.P1450P	CAGGGGTGGGGGG	.	4	4	0	0	T|0.010;C|0.990	48	0	48	0	0
ZNF517	340385	hgsc.bcm.edu	37	8	146033347	146033347	+	Missense_Mutation	SNP	T	T	C	rs2976653		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZNF517-90	NM_213605	exon5	c.T1046C	p.V349A	GCGGCGTGGGGCA	.	13	13	0	0	G|0.992;C|0.006	4	0	4	0	0
CDKN2A	1029	broad.mit.edu;bcgsc.ca	37	9	21974723	21974738	+	Frame_Shift_Del	DEL	CCCGCCTCCAGCAGCG	CCCGCCTCCAGCAGCG	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	CDKN2A-23992	NM_058197	exon1	c.89_104del	p.30_35del	AGCGCCCCCGCCT	.	26	4	43	0	.	0	0	0	0	0
ZCCHC6	79670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	88938270	88938270	+	Missense_Mutation	SNP	C	C	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	ZCCHC6-92	NM_024617	exon13	c.G2395A	p.E799K	CACACTCTTTAGC	.	84	18	83	0	.	1	1	0	0	0
CCDC180	0	broad.mit.edu	37	9	100079354	100079354	+	Missense_Mutation	SNP	A	A	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_020893	exon9	c.A935C	p.N312T	TCATGAACTATGC	.	93	4	105	0	.	0	0	0	0	0
GABBR2	9568	bcgsc.ca	37	9	101068580	101068580	+	Silent	SNP	G	G	A	rs2304389	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	GABBR2-518	NM_005458	exon15	c.C2052T	p.P684P	GAGTGCGGGGATG	.	378	10	424	1	G|0.831;A|0.169	0	0	0	0	0
AKAP2	11217	hgsc.bcm.edu	37	9	112811038	112811038	+	Missense_Mutation	SNP	C	C	T	rs78923754	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	AKAP2-24	NM_001004065	exon1	c.C59T	p.P20L	GACCCCCGGAGTC	.	12	8	0	0	C|0.917;T|0.083	0	0	0	0	0
SNAPC4	6621	broad.mit.edu	37	9	139277995	139277997	+	In_Frame_Del	DEL	GCT	GCT	-	rs34222232	alternate_allele	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SNAPC4-90	NM_003086	exon15	c.1624_1626del	p.542_542del	CTCCTCGCTGCTG	.	165	7	45	0	.	0	0	0	0	0
MAP3K15	389840	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	19428068	19428068	+	Silent	SNP	A	A	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	MAP3K15-335	NM_001001671	exon12	c.T1722C	p.F574F	GGCTGTAAAATTC	.	80	19	58	0	.	5	5	0	0	0
SUPT20HL1	100130302	bcgsc.ca	37	X	24382429	24382443	+	In_Frame_Del	DEL	CCTGCTCCTGCTCTA	CCTGCTCCTGCTCTA	-	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	CCTGCTCCTGCTCTA	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_001136234	exon1	c.1552_1566del	p.518_522del	GCTGCTCCTGCTC	.	257	92	310	0	.	0	0	0	0	0
SUPT20HL1	100130302	bcgsc.ca	37	X	24382453	24382453	+	Missense_Mutation	SNP	G	G	C	rs112697166		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	.	NM_001136234	exon1	c.G1576C	p.A526P	GCTGCTGCTGCTC	.	237	66	251	0	G|0.500;C|0.500	0	0	0	0	0
FAM47C	442444	broad.mit.edu	37	X	37028425	37028425	+	Missense_Mutation	SNP	A	A	G	rs145580328	byfrequency	TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FAM47C-111	NM_001013736	exon1	c.A1942G	p.N648D	CCTCCCAATACTG	.	107	3	98	0	A|1.000;G|0.000	0	0	0	0	0
UBQLN2	29978	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	56591776	56591776	+	Silent	SNP	C	C	G	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	UBQLN2-131	NM_013444	exon1	c.C1470G	p.G490G	TATAGGCCCTGTA	.	69	21	88	0	.	40	40	0	0	0
FLJ44635	0	bcgsc.ca	37	X	71379853	71379853	+	Silent	SNP	C	C	T	rs7880917		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	FLJ44635-108	NM_207422	exon2	c.C174T	p.S58S	TGCCTCCGCTGAA	.	355	9	381	2	C|0.581;T|0.419	3	3	0	0	0
RBM41	55285	broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	106358708	106358708	+	Missense_Mutation	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	RBM41-131	NM_001171080	exon4	c.C397T	p.R133C	GAATGCGCTGACG	.	107	50	121	1	.	1	1	0	0	0
PAK3	5063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	110395637	110395637	+	Splice_Site	SNP	G	G	A	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	PAK3-1043	NM_001128166	exon6	c.431-1G>A	.	TTTGCAGATAAAA	.	116	37	164	0	.	0	0	0	0	0
AVPR2	554	broad.mit.edu	37	X	153171451	153171451	+	Missense_Mutation	SNP	G	G	T	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	AVPR2-625	NM_001146151	exon2	c.G491T	p.W164L	TGGCTTGGGCCTT	.	79	12	66	10	.	0	0	0	0	0
SHANK3	85358	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	22	51144507	51144508	+	Frame_Shift_Ins	INS	-	-	C	novel		TCGA-OR-A5JM-01A-11D-A29I-10	TCGA-OR-A5JM-10B-01D-A29L-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.	.	Illumina GAIIx	a8935e4c-a863-4168-82a5-bcaaaf194e6d	4f8cbee5-63de-4167-8bd7-530ad1d3d2a0	.	SHANK3-69	NM_033517	exon17	c.1995_1996insC	p.P665fs	CCCACCGCCCCCC	.	112	38	96	0	.	0	0	0	0	0