#chr pos rsID ref alt score PASS detail gene gene_id transcript_id Dominant Loftol Recessive Maximum 1 55182300 . T A 1587.77 PASS AC=2;AF=1.00;AN=2;DP=41;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.24;VQSLOD=5.02;culprit=FS;CSQ=A|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|MROH7-TTC4|ENSG00000271723|Transcript|ENST00000425300|nonsense_mediated_decay|25/33||||4270/6090|-/1959|-/652|||||1||SNV|HGNC|49180|,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|MROH7-TTC4|ENSG00000271723|Transcript|ENST00000460155|retained_intron|9/17||||1818/3561|||||||1||SNV|HGNC|49180|,A|stop_gained&NMD_transcript_variant|HIGH|MROH7-TTC4|ENSG00000271723|Transcript|ENST00000414150|nonsense_mediated_decay|25/33||||4124/5867|3846/4005|1282/1334|C/*|tgT/tgA|||1||SNV|HGNC|49180|,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|TTC4|ENSG00000243725|Transcript|ENST00000371284|processed_transcript|2/10||||305/2124|||||||1||SNV|HGNC|12394|,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|TTC4|ENSG00000243725|Transcript|ENST00000486621|retained_intron|2/3||||183/549|||||||1||SNV|HGNC|12394|,A|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|MROH7-TTC4|ENSG00000271723|Transcript|ENST00000606515|nonsense_mediated_decay|24/33||||4022/5162|-/1884|-/627|||||1||SNV|HGNC|49180|,A|missense_variant|MODERATE|TTC4|ENSG00000243725|Transcript|ENST00000371281|protein_coding|2/10||||226/2395|139/1164|47/387|S/T|Tcg/Acg|||1|1|SNV|HGNC|12394|NM_004623.4 MROH7-TTC4 ENSG00000271723 ENST00000414150 0.0058 0.89545 0.09875 Tolerant 1 57209907 . C A 537.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.819;ClippingRankSum=-0.018;DP=34;FS=1.356;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.270;QD=15.82;ReadPosRankSum=-0.378;VQSLOD=2.82;culprit=FS;CSQ=A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|C1orf168|ENSG00000187889|Transcript|ENST00000493000|processed_transcript|6/14||||427/1904|||||||-1||SNV|HGNC|27295|,A|stop_gained|HIGH|C1orf168|ENSG00000187889|Transcript|ENST00000343433|protein_coding|10/20||||1501/3135|1420/2187|474/728|E/*|Gaa/Taa|||-1|1|SNV|HGNC|27295|NM_001004303.4,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|C1orf168|ENSG00000187889|Transcript|ENST00000484327|processed_transcript|7/14||||1662/2151|||||||-1||SNV|HGNC|27295| C1orf168 ENSG00000187889 ENST00000343433 0.0125 0.9429 0.0446 Tolerant 1 152323132 . G T 899.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.374;ClippingRankSum=0.096;DP=49;FS=2.485;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.952;POSITIVE_TRAIN_SITE;QD=18.36;ReadPosRankSum=0.353;VQSLOD=3.35;culprit=FS;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000392688|antisense||6/6|||-/2995|||||||1||SNV|HGNC|27913|,T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000445097|antisense||2/2|||-/2852|||||||1||SNV|HGNC|27913|,T|stop_gained|HIGH|FLG2|ENSG00000143520|Transcript|ENST00000388718|protein_coding|3/3||||7203/9124|7130/7176|2377/2391|S/*|tCa/tAa|||-1|1|SNV|HGNC|33276|NM_001014342.2 FLG2 ENSG00000143520 ENST00000388718 0.00315 0.9745 0.02235 Tolerant 1 159785413 . C T 503.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.758;ClippingRankSum=-0.816;DP=43;FS=2.756;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.230;POSITIVE_TRAIN_SITE;QD=11.72;ReadPosRankSum=-0.816;VQSLOD=3.60;culprit=MQRankSum;CSQ=T|downstream_gene_variant|MODIFIER|FCRL6|ENSG00000181036|Transcript|ENST00000392235|protein_coding|||||-/947|-/936|-/311||||31|1||SNV|HGNC|31910|,T|3_prime_UTR_variant|MODIFIER|FCRL6|ENSG00000181036|Transcript|ENST00000339348|protein_coding|9/9||||1243/1422|-/1194|-/397|||||1||SNV|HGNC|31910|,T|3_prime_UTR_variant|MODIFIER|FCRL6|ENSG00000181036|Transcript|ENST00000321935|protein_coding|11/11||||1369/1997|-/1242|-/413|||||1||SNV|HGNC|31910|NM_001284217.1,T|stop_gained|HIGH|FCRL6|ENSG00000181036|Transcript|ENST00000368106|protein_coding|10/10||||1268/1306|1267/1305|423/434|Q/*|Caa/Taa|||1|1|SNV|HGNC|31910|NM_001004310.2 FCRL6 ENSG00000181036 ENST00000368106 0.00045 0.9945 0.00505 Tolerant 1 223722780 . G A 1993.77 PASS AC=2;AF=1.00;AN=2;DP=52;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.32;VQSLOD=5.35;culprit=FS;CSQ=A|intron_variant|MODIFIER|CAPN8|ENSG00000203697|Transcript|ENST00000430824|protein_coding||1/6|||-/695|-/471|-/156|||||-1||SNV|HGNC|1485|,A|upstream_gene_variant|MODIFIER|CAPN8|ENSG00000203697|Transcript|ENST00000482401|retained_intron|||||-/1023||||||4044|-1||SNV|HGNC|1485|,A|stop_gained|HIGH|CAPN8|ENSG00000203697|Transcript|ENST00000366872|protein_coding|14/20||||1612/2262|1612/2046|538/681|R/*|Cga/Tga|||-1|1|SNV|HGNC|1485|,A|intron_variant|MODIFIER|CAPN8|ENSG00000203697|Transcript|ENST00000442247|protein_coding||1/3|||-/327|-/306|-/101|||||-1||SNV|HGNC|1485| CAPN8 ENSG00000203697 ENST00000366872 0.00175 0.98475 0.0135 Tolerant 1 225528175 . G T 399.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.815;ClippingRankSum=1.385;DP=42;FS=3.005;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.581;POSITIVE_TRAIN_SITE;QD=9.52;ReadPosRankSum=-0.611;VQSLOD=3.23;culprit=QD;CSQ=T|stop_gained&NMD_transcript_variant|HIGH|DNAH14|ENSG00000185842|Transcript|ENST00000327794|nonsense_mediated_decay|25/40||||3347/8488|3349/4446|1117/1481|E/*|Gaa/Taa|||1||SNV|HGNC|2945|,T|stop_gained|HIGH|DNAH14|ENSG00000185842|Transcript|ENST00000445597|protein_coding|47/61||||7762/10524|7762/10524|2588/3507|E/*|Gaa/Taa|||1||SNV|HGNC|2945|,T|stop_gained|HIGH|DNAH14|ENSG00000185842|Transcript|ENST00000430092|protein_coding|67/84||||10386/13788|10171/13548|3391/4515|E/*|Gaa/Taa|||1|1|SNV|HGNC|2945|NM_001373.1,T|stop_gained|HIGH|DNAH14|ENSG00000185842|Transcript|ENST00000439375|protein_coding|66/83||||10171/13548|10171/13548|3391/4515|E/*|Gaa/Taa|||1||SNV|HGNC|2945| DNAH14 ENSG00000185842 ENST00000430092 0.0079 0.92225 0.06985 Tolerant 1 228391808 . G T 564.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.421;ClippingRankSum=-1.061;DP=31;FS=3.151;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.100;POSITIVE_TRAIN_SITE;QD=18.22;ReadPosRankSum=1.701;VQSLOD=3.31;culprit=FS;CSQ=T|upstream_gene_variant|MODIFIER|OBSCN|ENSG00000154358|Transcript|ENST00000366707|protein_coding|||||-/25575|-/16809|-/5602||||4053|1||SNV|HGNC|15719|,T|downstream_gene_variant|MODIFIER|C1orf145|ENSG00000162913|Transcript|ENST00000337335|nonsense_mediated_decay|||||-/2893|-/477|-/158||||359|-1||SNV|HGNC|32047|,T|upstream_gene_variant|MODIFIER|OBSCN|ENSG00000154358|Transcript|ENST00000366709|protein_coding|||||-/19907|-/11220|-/3739||||4053|1||SNV|HGNC|15719|,T|upstream_gene_variant|MODIFIER|OBSCN|ENSG00000154358|Transcript|ENST00000284548|protein_coding|||||-/20432|-/19863|-/6620||||4023|1||SNV|HGNC|15719|NM_052843.3,T|stop_gained|HIGH|C1orf145|ENSG00000162913|Transcript|ENST00000295012|protein_coding|2/2||||288/889|288/342|96/113|Y/*|taC/taA|||-1|1|SNV|HGNC|32047|,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|C1orf145|ENSG00000162913|Transcript|ENST00000472613|nonsense_mediated_decay|4/4||||502/624|-/288|-/95|||||-1||SNV|HGNC|32047|,T|upstream_gene_variant|MODIFIER|OBSCN|ENSG00000154358|Transcript|ENST00000570156|protein_coding|||||-/26927|-/26772|-/8923||||4023|1||SNV|HGNC|15719|NM_001271223.2,T|upstream_gene_variant|MODIFIER|OBSCN|ENSG00000154358|Transcript|ENST00000422127|protein_coding|||||-/24030|-/23907|-/7968||||4053|1||SNV|HGNC|15719|NM_001098623.2 C1orf145 ENSG00000162913 ENST00000295012 0.0074 0.97155 0.02105 Tolerant 1 248113026 . T A 917.77 PASS AC=2;AF=1.00;AN=2;DP=26;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=31.50;VQSLOD=3.78;culprit=FS;CSQ=A|stop_gained|HIGH|OR2L8|ENSG00000196936|Transcript|ENST00000357191|protein_coding|1/1||||867/939|867/939|289/312|Y/*|taT/taA|||1|1|SNV|HGNC|15014|NM_001001963.1,A|intron_variant|MODIFIER|OR2L13|ENSG00000196071|Transcript|ENST00000366478|protein_coding||1/2|||-/1883|-/939|-/312|||||1||SNV|HGNC|19578|NM_175911.2 OR2L8 ENSG00000196936 ENST00000357191 1e-04 0.99385 0.00605 Tolerant 2 3212704 . C A 687.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.474;ClippingRankSum=0.198;DP=31;FS=1.494;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.550;POSITIVE_TRAIN_SITE;QD=22.19;ReadPosRankSum=-0.110;VQSLOD=2.57;culprit=FS;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000482570|retained_intron||2/3|||-/582|||||||-1||SNV|HGNC|12383|,A|intron_variant&non_coding_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000463662|processed_transcript||4/5|||-/757|||||||-1||SNV|HGNC|12383|,A|intron_variant&non_coding_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000470625|retained_intron||1/1|||-/411|||||||-1||SNV|HGNC|12383|,A|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000441271|protein_coding||2/4|||-/647|-/536|-/178|||||-1||SNV|HGNC|12383|,A|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000398659|protein_coding||6/9|||-/1795|-/1245|-/414|||||-1||SNV|HGNC|12383|,A|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000382125|protein_coding||5/8|||-/1766|-/1164|-/387|||||-1|1|SNV|HGNC|12383|NM_003310.2,A|stop_gained|HIGH|TSSC1|ENSG00000032389|Transcript|ENST00000443925|protein_coding|6/6||||642/1771|541/945|181/314|G/*|Gga/Tga|||-1||SNV|HGNC|12383|,A|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000455162|nonsense_mediated_decay||3/6|||-/847|-/177|-/58|||||-1||SNV|HGNC|12383|,A|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000435721|nonsense_mediated_decay||4/5|||-/672|-/399|-/132|||||-1||SNV|HGNC|12383|,A|intron_variant&non_coding_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000478754|processed_transcript||7/10|||-/2932|||||||-1||SNV|HGNC|12383| TSSC1 ENSG00000032389 ENST00000443925 0.01745 0.90505 0.0775 Tolerant 2 6112516 . C T 997.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.098;ClippingRankSum=0.339;DP=49;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.605;POSITIVE_TRAIN_SITE;QD=20.36;ReadPosRankSum=-0.482;VQSLOD=5.09;culprit=FS;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01105|ENSG00000232044|Transcript|ENST00000456327|lincRNA||3/4|||-/1434|||||||1||SNV|HGNC|26403|,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01105|ENSG00000232044|Transcript|ENST00000431188|lincRNA||2/4|||-/3329|||||||1||SNV|HGNC|26403|,T|stop_gained|HIGH|DKFZP761K2322|ENSG00000272268|Transcript|ENST00000391666|protein_coding|1/1||||805/2663|460/480|154/159|Q/*|Caa/Taa|||1|1|SNV|Uniprot_gn|| DKFZP761K2322 ENSG00000272268 ENST00000391666 0.01495 0.8482 0.13685 Tolerant 2 120125053 . C G 570.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.058;ClippingRankSum=0.565;DP=33;FS=5.287;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.164;POSITIVE_TRAIN_SITE;QD=17.30;ReadPosRankSum=-0.637;VQSLOD=2.73;culprit=FS;CSQ=G|upstream_gene_variant|MODIFIER|C2orf76|ENSG00000186132|Transcript|ENST00000409523|protein_coding|||||-/747|-/381|-/126||||795|-1||SNV|HGNC|27017|,G|stop_gained|HIGH|DBI|ENSG00000155368|Transcript|ENST00000542275|protein_coding|1/4||||225/753|141/447|47/148|Y/*|taC/taG|||1|1|SNV|HGNC|2690|NM_001178017.1,G|intron_variant|MODIFIER|DBI|ENSG00000155368|Transcript|ENST00000311521|protein_coding||1/4|||-/714|-/315|-/104|||||1||SNV|HGNC|2690|NM_001282635.1,G|upstream_gene_variant|MODIFIER|C2orf76|ENSG00000186132|Transcript|ENST00000334816|protein_coding|||||-/676|-/381|-/126||||649|-1||SNV|HGNC|27017|,G|upstream_gene_variant|MODIFIER|DBI|ENSG00000155368|Transcript|ENST00000475783|retained_intron|||||-/842||||||2740|1||SNV|HGNC|2690|,G|intron_variant|MODIFIER|DBI|ENSG00000155368|Transcript|ENST00000409094|protein_coding||1/4|||-/576|-/315|-/104|||||1||SNV|HGNC|2690|NM_001282634.1,G|intron_variant|MODIFIER|DBI|ENSG00000155368|Transcript|ENST00000535757|protein_coding||1/4|||-/672|-/315|-/104|||||1||SNV|HGNC|2690|NM_001178042.1&NM_020548.6&NM_001282633.1,G|upstream_gene_variant|MODIFIER|C2orf76|ENSG00000186132|Transcript|ENST00000409877|protein_coding|||||-/950|-/381|-/126||||795|-1||SNV|HGNC|27017|NM_001017927.2,G|stop_gained|HIGH|DBI|ENSG00000155368|Transcript|ENST00000535617|protein_coding|2/5||||159/687|84/390|28/129|Y/*|taC/taG|||1||SNV|HGNC|2690|NM_001178041.1,G|upstream_gene_variant|MODIFIER|DBI|ENSG00000155368|Transcript|ENST00000393103|protein_coding|||||-/599|-/267|-/88||||200|1||SNV|HGNC|2690|NM_001079863.1,G|intron_variant|MODIFIER|DBI|ENSG00000155368|Transcript|ENST00000355857|protein_coding||1/3|||-/627|-/264|-/87|||||1||SNV|HGNC|2690|NM_001178043.1&NM_001079862.1,G|upstream_gene_variant|MODIFIER|C2orf76|ENSG00000186132|Transcript|ENST00000414534|protein_coding|||||-/509|-/256|-/85||||714|-1||SNV|HGNC|27017|,G|intron_variant&non_coding_transcript_variant|MODIFIER|DBI|ENSG00000155368|Transcript|ENST00000460901|processed_transcript||1/3|||-/774|||||||1||SNV|HGNC|2690|,G|intron_variant&non_coding_transcript_variant|MODIFIER|DBI|ENSG00000155368|Transcript|ENST00000492375|retained_intron||1/1|||-/784|||||||1||SNV|HGNC|2690|,G|upstream_gene_variant|MODIFIER|C2orf76|ENSG00000186132|Transcript|ENST00000498049|processed_transcript|||||-/440||||||652|-1||SNV|HGNC|27017|,G|upstream_gene_variant|MODIFIER|C2orf76|ENSG00000186132|Transcript|ENST00000409466|protein_coding|||||-/1150|-/381|-/126||||735|-1||SNV|HGNC|27017| DBI ENSG00000155368 ENST00000542275 0.0118 0.9218 0.0664 Tolerant 2 183995729 . C T 669.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.948;ClippingRankSum=-3.006;DP=40;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.515;POSITIVE_TRAIN_SITE;QD=16.74;ReadPosRankSum=2.817;VQSLOD=5.34;culprit=FS;CSQ=T|downstream_gene_variant|MODIFIER|NUP35|ENSG00000163002|Transcript|ENST00000455063|protein_coding|||||-/342|-/160|-/53||||2544|1||SNV|HGNC|29797|,T|intron_variant|MODIFIER|NUP35|ENSG00000163002|Transcript|ENST00000446612|protein_coding||3/3|||-/470|-/346|-/115|||||1||SNV|HGNC|29797|,T|intron_variant|MODIFIER|NUP35|ENSG00000163002|Transcript|ENST00000295119|protein_coding||3/8|||-/1633|-/981|-/326|||||1|1|SNV|HGNC|29797|NM_138285.3&NM_001287584.1,T|intron_variant|MODIFIER|NUP35|ENSG00000163002|Transcript|ENST00000409798|protein_coding||4/9|||-/1470|-/930|-/309|||||1||SNV|HGNC|29797|,T|intron_variant&non_coding_transcript_variant|MODIFIER|NUP35|ENSG00000163002|Transcript|ENST00000479162|retained_intron||3/6|||-/2828|||||||1||SNV|HGNC|29797|,T|downstream_gene_variant|MODIFIER|NUP35|ENSG00000163002|Transcript|ENST00000442895|protein_coding|||||-/616|-/230|-/76||||514|1||SNV|HGNC|29797|,T|5_prime_UTR_variant|MODIFIER|NUP35|ENSG00000163002|Transcript|ENST00000541912|protein_coding|4/10||||359/1624|-/576|-/191|||||1||SNV|HGNC|29797|NM_001287585.1,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|NUP35|ENSG00000163002|Transcript|ENST00000497330|processed_transcript|4/4||||428/544|||||||1||SNV|HGNC|29797|,T|stop_gained&NMD_transcript_variant|HIGH|NUP35|ENSG00000163002|Transcript|ENST00000452137|nonsense_mediated_decay|4/5||||346/755|346/411|116/136|Q/*|Caa/Taa|||1||SNV|HGNC|29797|,T|intron_variant&NMD_transcript_variant|MODIFIER|NUP35|ENSG00000163002|Transcript|ENST00000374930|nonsense_mediated_decay||3/7|||-/998|-/459|-/152|||||1||SNV|HGNC|29797| NUP35 ENSG00000163002 ENST00000452137 0.03165 0.92625 0.0421 Tolerant 2 240500249 . C T 486.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.207;ClippingRankSum=-0.342;DP=34;FS=3.581;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.099;POSITIVE_TRAIN_SITE;QD=14.32;ReadPosRankSum=1.999;VQSLOD=2.88;culprit=FS;CSQ=T|stop_gained|HIGH|AC079612.1|ENSG00000196758|Transcript|ENST00000358775|protein_coding|1/2||||255/3700|130/591|44/196|R/*|Cga/Tga|||1|1|SNV|Clone_based_vega_gene|| AC079612.1 ENSG00000196758 ENST00000358775 0.0018 0.98205 0.01615 Tolerant 3 98031307 . T A 1946.77 PASS AC=2;AF=1.00;AN=2;DP=44;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.43;VQSLOD=5.69;culprit=FS;CSQ=A|stop_gained|HIGH|OR5H8P|ENSG00000232535|Transcript|ENST00000394191|polymorphic_pseudogene|1/1||||551/931|551/931|184/310|L/*|tTg/tAg|||1|1|SNV|HGNC|14773|,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-325B23.2|ENSG00000251088|Transcript|ENST00000508616|lincRNA||2/3|||-/392|||||||1||SNV|Clone_based_vega_gene|| OR5H8P ENSG00000232535 ENST00000394191 0.0285 0.7947 0.1768 Tolerant 3 194061907 . G A 1451.77 PASS AC=2;AF=1.00;AN=2;DP=33;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=26.30;VQSLOD=4.06;culprit=FS;CSQ=A|stop_gained|HIGH|CPN2|ENSG00000178772|Transcript|ENST00000323830|protein_coding|2/2||||1615/3028|1525/1638|509/545|Q/*|Cag/Tag|||-1|1|SNV|HGNC|2313|NM_001080513.2,A|stop_gained|HIGH|CPN2|ENSG00000178772|Transcript|ENST00000429275|protein_coding|2/2||||1602/2008|1525/1638|509/545|Q/*|Cag/Tag|||-1||SNV|HGNC|2313| CPN2 ENSG00000178772 ENST00000323830 0.00805 0.95145 0.0405 Tolerant 4 1090625 . G A 1230.77 PASS AC=2;AF=1.00;AN=2;DP=33;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.78;VQSLOD=5.95;culprit=FS;CSQ=A|splice_region_variant&non_coding_transcript_exon_variant&non_coding_transcript_variant|LOW|RNF212|ENSG00000178222|Transcript|ENST00000454487|retained_intron|3/3||||257/631|||||||-1||SNV|HGNC|27729|,A|stop_gained&splice_region_variant&NMD_transcript_variant|HIGH|RNF212|ENSG00000178222|Transcript|ENST00000508428|nonsense_mediated_decay|2/8||||163/804|112/159|38/52|R/*|Cga/Tga|||-1||SNV|HGNC|27729|,A|splice_region_variant&synonymous_variant|LOW|RNF212|ENSG00000178222|Transcript|ENST00000433731|protein_coding|3/10||||236/1074|174/894|58/297|T|acC/acT|||-1|1|SNV|HGNC|27729|,A|downstream_gene_variant|MODIFIER|RNF212|ENSG00000178222|Transcript|ENST00000505730|processed_transcript|||||-/488||||||4076|-1||SNV|HGNC|27729|,A|splice_region_variant&synonymous_variant&NMD_transcript_variant|LOW|RNF212|ENSG00000178222|Transcript|ENST00000511620|nonsense_mediated_decay|3/7||||236/926|174/372|58/123|T|acC/acT|||-1||SNV|HGNC|27729|,A|splice_region_variant&3_prime_UTR_variant&NMD_transcript_variant|LOW|RNF212|ENSG00000178222|Transcript|ENST00000510715|nonsense_mediated_decay|4/8||||463/934|-/348|-/115|||||-1||SNV|HGNC|27729|,A|stop_gained&splice_region_variant&NMD_transcript_variant|HIGH|RNF212|ENSG00000178222|Transcript|ENST00000506730|nonsense_mediated_decay|2/10||||188/753|112/159|38/52|R/*|Cga/Tga|||-1||SNV|HGNC|27729|,A|splice_region_variant&non_coding_transcript_exon_variant&non_coding_transcript_variant|LOW|RNF212|ENSG00000178222|Transcript|ENST00000512552|retained_intron|2/4||||148/522|||||||-1||SNV|HGNC|27729|,A|splice_region_variant&synonymous_variant|LOW|RNF212|ENSG00000178222|Transcript|ENST00000382968|protein_coding|3/10||||272/2332|174/699|58/232|T|acC/acT|||-1||SNV|HGNC|27729|NM_194439.4&NM_001131034.3,A|downstream_gene_variant|MODIFIER|RP11-20I20.1|ENSG00000251639|Transcript|ENST00000513176|processed_pseudogene|||||-/1204||||||3179|-1||SNV|Clone_based_vega_gene||,A|splice_region_variant&synonymous_variant|LOW|RNF212|ENSG00000178222|Transcript|ENST00000333673|protein_coding|3/4||||240/1019|174/822|58/273|T|acC/acT|||-1||SNV|HGNC|27729|NM_001193318.2 RNF212 ENSG00000178222 ENST00000508428 0.00335 0.97295 0.0237 Tolerant 4 106474097 . G T 675.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.925;ClippingRankSum=-0.436;DP=39;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.110;QD=17.33;ReadPosRankSum=0.295;VQSLOD=3.57;culprit=FS;CSQ=T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|ARHGEF38|ENSG00000236699|Transcript|ENST00000506828|processed_transcript|1/4||||48/492|||||||1||SNV|HGNC|25968|,T|stop_gained|HIGH|ARHGEF38|ENSG00000236699|Transcript|ENST00000265154|protein_coding|1/4||||321/1437|175/660|59/219|E/*|Gaa/Taa|||1||SNV|HGNC|25968|NM_017700.1,T|upstream_gene_variant|MODIFIER|AC004066.3|ENSG00000250522|Transcript|ENST00000514879|antisense|||||-/572||||||585|-1||SNV|Clone_based_vega_gene||,T|stop_gained|HIGH|ARHGEF38|ENSG00000236699|Transcript|ENST00000420470|protein_coding|1/14||||319/5454|175/2334|59/777|E/*|Gaa/Taa|||1|1|SNV|HGNC|25968|NM_001242729.1 ARHGEF38 ENSG00000236699 ENST00000420470 0.0363 0.50895 0.45475 Tolerant 5 33751454 . A T 869.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.954;ClippingRankSum=-1.505;DP=45;FS=2.650;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.563;POSITIVE_TRAIN_SITE;QD=19.33;ReadPosRankSum=0.839;VQSLOD=3.42;culprit=QD;CSQ=T|stop_gained|HIGH|ADAMTS12|ENSG00000151388|Transcript|ENST00000515401|protein_coding|3/3||||852/1003|689/699|230/232|L/*|tTg/tAg|||-1||SNV|HGNC|14605|,T|intron_variant|MODIFIER|ADAMTS12|ENSG00000151388|Transcript|ENST00000504830|protein_coding||3/23|||-/8774|-/4785|-/1594|||||-1|1|SNV|HGNC|14605|NM_030955.2,T|intron_variant&non_coding_transcript_variant|MODIFIER|ADAMTS12|ENSG00000151388|Transcript|ENST00000504582|processed_transcript||2/17|||-/2743|||||||-1||SNV|HGNC|14605|,T|intron_variant|MODIFIER|ADAMTS12|ENSG00000151388|Transcript|ENST00000352040|protein_coding||3/21|||-/4622|-/4530|-/1509|||||-1||SNV|HGNC|14605| ADAMTS12 ENSG00000151388 ENST00000515401 0.0069 0.93425 0.05885 Tolerant 5 74965122 . G A 1421.77 PASS AC=2;AF=1.00;AN=2;DP=36;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.70;VQSLOD=5.41;culprit=FS;CSQ=A|downstream_gene_variant|MODIFIER|POC5|ENSG00000152359|Transcript|ENST00000514838|protein_coding|||||-/1984|-/1644|-/547||||4905|-1||SNV|HGNC|26658|,A|stop_gained|HIGH|ANKDD1B|ENSG00000189045|Transcript|ENST00000601380|protein_coding|13/14||||1615/2569|1439/1587|480/528|W/*|tGg/tAg|||1|1|SNV|HGNC|32525|NM_001276713.1,A|intron_variant&non_coding_transcript_variant|MODIFIER|ANKDD1B|ENSG00000189045|Transcript|ENST00000506596|processed_transcript||6/6|||-/1815|||||||1||SNV|HGNC|32525|,A|downstream_gene_variant|MODIFIER|POC5|ENSG00000152359|Transcript|ENST00000380475|protein_coding|||||-/1975|-/1200|-/399||||4911|-1||SNV|HGNC|26658|,A|downstream_gene_variant|MODIFIER|POC5|ENSG00000152359|Transcript|ENST00000428202|protein_coding|||||-/2229|-/1728|-/575||||4827|-1||SNV|HGNC|26658|NM_001099271.1 ANKDD1B ENSG00000189045 ENST00000601380 0.0163 0.80065 0.18305 Tolerant 5 79731608 . G A 1812.77 PASS AC=2;AF=1.00;AN=2;DP=47;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=34.68;VQSLOD=5.20;culprit=FS;CSQ=A|intron_variant|MODIFIER|ZFYVE16|ENSG00000039319|Transcript|ENST00000338008|protein_coding||2/17|||-/6773|-/4620|-/1539|||||1|1|SNV|HGNC|20756|NM_014733.3&NM_001284236.1,A|intron_variant&non_coding_transcript_variant|MODIFIER|ZFYVE16|ENSG00000039319|Transcript|ENST00000510995|retained_intron||2/3|||-/2873|||||||1||SNV|HGNC|20756|,A|intron_variant|MODIFIER|ZFYVE16|ENSG00000039319|Transcript|ENST00000505560|protein_coding||3/18|||-/6599|-/4620|-/1539|||||1||SNV|HGNC|20756|,A|stop_gained&NMD_transcript_variant|HIGH|ZFYVE16|ENSG00000039319|Transcript|ENST00000509562|nonsense_mediated_decay|3/4||||215/684|98/105|33/34|W/*|tGg/tAg|||1||SNV|HGNC|20756|,A|intron_variant|MODIFIER|ZFYVE16|ENSG00000039319|Transcript|ENST00000510158|protein_coding||3/18|||-/6680|-/4620|-/1539|||||1||SNV|HGNC|20756|NM_001105251.1,A|intron_variant&non_coding_transcript_variant|MODIFIER|ZFYVE16|ENSG00000039319|Transcript|ENST00000512558|retained_intron||2/9|||-/4496|||||||1||SNV|HGNC|20756| ZFYVE16 ENSG00000039319 ENST00000509562 0.0101 0.95615 0.03375 Tolerant 5 134782450 . T A 1075.77 PASS AC=2;AF=1.00;AN=2;DP=28;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=27.97;VQSLOD=5.90;culprit=FS;CSQ=A|upstream_gene_variant|MODIFIER|CTB-138E5.1|ENSG00000249639|Transcript|ENST00000510230|antisense|||||-/504||||||3853|1||SNV|Clone_based_vega_gene||,A|3_prime_UTR_variant|MODIFIER|TIFAB|ENSG00000255833|Transcript|ENST00000537858|protein_coding|2/2||||3381/5923|-/486|-/161|||||-1||SNV|HGNC|34024|NM_001099221.1,A|stop_gained|HIGH|C5orf20|ENSG00000251380|Transcript|ENST00000503143|protein_coding|1/1||||589/3134|349/735|117/244|R/*|Aga/Tga|||-1|1|SNV|HGNC|24459|NM_130848.2 C5orf20 ENSG00000251380 ENST00000503143 0.00205 0.9868 0.01115 Tolerant 6 3255327 . G A 1780.77 PASS AC=2;AF=1.00;AN=2;DP=47;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=23.53;VQSLOD=4.22;culprit=FS;CSQ=A|upstream_gene_variant|MODIFIER|PSMG4|ENSG00000180822|Transcript|ENST00000454610|protein_coding|||||-/2323|-/354|-/117||||3967|1||SNV|HGNC|21108|,A|upstream_gene_variant|MODIFIER|PSMG4|ENSG00000180822|Transcript|ENST00000451246|protein_coding|||||-/824|-/231|-/76||||3891|1||SNV|HGNC|21108|,A|upstream_gene_variant|MODIFIER|PSMG4|ENSG00000180822|Transcript|ENST00000324987|nonsense_mediated_decay|||||-/778|-/327|-/108||||3884|1||SNV|HGNC|21108|,A|upstream_gene_variant|MODIFIER|PSMG4|ENSG00000180822|Transcript|ENST00000438998|protein_coding|||||-/838|-/372|-/123||||3801|1||SNV|HGNC|21108|NM_001128591.1,A|upstream_gene_variant|MODIFIER|PSMG4|ENSG00000180822|Transcript|ENST00000419065|protein_coding|||||-/629|-/489|-/162||||3859|1|1|SNV|HGNC|21108|NM_001128592.1,A|intron_variant&NMD_transcript_variant|MODIFIER|PSMG4|ENSG00000180822|Transcript|ENST00000509933|nonsense_mediated_decay||2/2|||-/2241|-/108|-/35|||||1||SNV|HGNC|21108|,A|stop_gained|HIGH|PSMG4|ENSG00000180822|Transcript|ENST00000380306|protein_coding|2/3||||399/726|117/375|39/124|W/*|tgG/tgA|||1||SNV|HGNC|21108|,A|upstream_gene_variant|MODIFIER|PSMG4|ENSG00000180822|Transcript|ENST00000380305|protein_coding|||||-/489|-/249|-/82||||3804|1||SNV|HGNC|21108|,A|upstream_gene_variant|MODIFIER|PSMG4|ENSG00000180822|Transcript|ENST00000473000|protein_coding|||||-/4603|-/315|-/104||||3868|1||SNV|HGNC|21108|NM_001135750.1 PSMG4 ENSG00000180822 ENST00000380306 0.0027 0.97835 0.01895 Tolerant 6 17606162 . C T 509.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.038;ClippingRankSum=0.013;DP=42;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.302;QD=12.14;ReadPosRankSum=-0.696;VQSLOD=4.43;culprit=FS;CSQ=T|stop_gained|HIGH|FAM8A1|ENSG00000137414|Transcript|ENST00000259963|protein_coding|4/5||||1070/4677|1015/1242|339/413|R/*|Cga/Tga|||1|1|SNV|HGNC|16372|NM_016255.2 FAM8A1 ENSG00000137414 ENST00000259963 0.4044 0.05635 0.53925 Recessive 6 31124849 . C T 591.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.502;ClippingRankSum=1.172;DP=35;FS=3.012;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.281;POSITIVE_TRAIN_SITE;QD=16.91;ReadPosRankSum=-0.215;VQSLOD=3.78;culprit=FS;CSQ=T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000505392|retained_intron|2/4||||46/547|||||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000502557|protein_coding|2/4||||273/662|-/356|-/118|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000448162|protein_coding|2/5||||101/699|-/565|-/188|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000508683|protein_coding|2/5||||55/567|-/479|-/159|||||-1||SNV|HGNC|13930|,T|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000542218|protein_coding|||||-/805|-/654|-/217||||4377|1||SNV|HGNC|11629|,T|5_prime_UTR_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000508852|nonsense_mediated_decay|2/5||||46/589|-/243|-/80|||||-1||SNV|HGNC|13930|,T|stop_gained|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000426967|protein_coding|2/4||||449/838|261/650|87/216|W/*|tgG/tgA|||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000455279|protein_coding|3/5||||185/676|-/458|-/152|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507226|protein_coding|3/5||||223/544|-/288|-/96|||||-1||SNV|HGNC|13930|,T|stop_gained|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000451521|protein_coding|2/18||||241/2587|234/2508|78/835|W/*|tgG/tgA|||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507829|protein_coding|3/5||||209/589|-/347|-/115|||||-1||SNV|HGNC|13930|,T|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000376257|protein_coding|||||-/3290|-/1038|-/345||||1470|1||SNV|HGNC|11629|NM_007109.2,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000396263|protein_coding|2/16||||119/2490|-/2190|-/729|||||-1||SNV|HGNC|13930|,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000509552|retained_intron|2/14||||108/2304|||||||-1||SNV|HGNC|13930|,T|upstream_gene_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000464012|retained_intron|||||-/512||||||2321|-1||SNV|HGNC|13930|,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000480060|processed_transcript|2/3||||43/601|||||||-1||SNV|HGNC|13930|,T|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000496421|processed_transcript|||||-/880||||||4412|1||SNV|HGNC|11629|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507751|protein_coding|2/4||||81/588|-/474|-/158|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000506831|protein_coding|1/2||||720/861|-/108|-/36|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507459|nonsense_mediated_decay|2/5||||42/582|-/243|-/80|||||-1||SNV|HGNC|13930|,T|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000376255|protein_coding|||||-/3039|-/1038|-/345||||1475|1||SNV|HGNC|11629|NM_001077511.1,T|stop_gained|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000396268|protein_coding|2/18||||423/2958|234/2616|78/871|W/*|tgG/tgA|||-1|1|SNV|HGNC|13930|NM_001105563.1&NM_001105564.1,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000475684|retained_intron|2/3||||24/786|||||||-1||SNV|HGNC|13930|,T|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000513222|protein_coding||1/2|||-/511|-/421|-/140|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000448141|protein_coding|2/5||||57/664|-/574|-/191|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507892|protein_coding|3/4||||323/479|-/123|-/41|||||-1||SNV|HGNC|13930|,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000488920|nonsense_mediated_decay|2/3||||472/715|-/243|-/80|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000503934|protein_coding|2/4||||108/560|-/419|-/139|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000512418|nonsense_mediated_decay|2/6||||46/565|-/135|-/44|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000428174|protein_coding|2/3||||57/470|-/380|-/126|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000503420|protein_coding|2/4||||168/580|-/379|-/126|||||-1||SNV|HGNC|13930|,T|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000376266|protein_coding|2/18||||90/2625|-/2349|-/782|||||-1||SNV|HGNC|13930|NM_019052.3 CCHCR1 ENSG00000204536 ENST00000396268 0.01315 0.93225 0.0546 Tolerant 6 31125257 . C A 863.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.872;ClippingRankSum=0.875;DP=46;FS=11.017;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.942;POSITIVE_TRAIN_SITE;QD=18.78;ReadPosRankSum=-0.897;VQSLOD=1.29;culprit=FS;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000505392|retained_intron||1/3|||-/547|||||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000502557|protein_coding||1/3|||-/662|-/356|-/118|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000448162|protein_coding||1/4|||-/699|-/565|-/188|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000508683|protein_coding||1/4|||-/567|-/479|-/159|||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000542218|protein_coding|||||-/805|-/654|-/217||||3969|1||SNV|HGNC|11629|,A|intron_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000508852|nonsense_mediated_decay||1/4|||-/589|-/243|-/80|||||-1||SNV|HGNC|13930|,A|stop_gained|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000426967|protein_coding|1/4||||309/838|121/650|41/216|E/*|Gaa/Taa|||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000455279|protein_coding|2/5||||72/676|-/458|-/152|||||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507226|protein_coding|2/5||||44/544|-/288|-/96|||||-1||SNV|HGNC|13930|,A|stop_gained|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000451521|protein_coding|1/18||||128/2587|121/2508|41/835|E/*|Gaa/Taa|||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507829|protein_coding|2/5||||69/589|-/347|-/115|||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000376257|protein_coding|||||-/3290|-/1038|-/345||||1062|1||SNV|HGNC|11629|NM_007109.2,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000396263|protein_coding||1/15|||-/2490|-/2190|-/729|||||-1||SNV|HGNC|13930|,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000509552|retained_intron||1/13|||-/2304|||||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000464012|retained_intron|||||-/512||||||2729|-1||SNV|HGNC|13930|,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000480060|processed_transcript||1/2|||-/601|||||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000496421|processed_transcript|||||-/880||||||4004|1||SNV|HGNC|11629|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507751|protein_coding||1/3|||-/588|-/474|-/158|||||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000506831|protein_coding|1/2||||312/861|-/108|-/36|||||-1||SNV|HGNC|13930|,A|intron_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507459|nonsense_mediated_decay||1/4|||-/582|-/243|-/80|||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000376255|protein_coding|||||-/3039|-/1038|-/345||||1067|1||SNV|HGNC|11629|NM_001077511.1,A|stop_gained|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000396268|protein_coding|1/18||||310/2958|121/2616|41/871|E/*|Gaa/Taa|||-1|1|SNV|HGNC|13930|NM_001105563.1&NM_001105564.1,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000475684|retained_intron||1/2|||-/786|||||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000513222|protein_coding||1/2|||-/511|-/421|-/140|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000448141|protein_coding||1/4|||-/664|-/574|-/191|||||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507892|protein_coding|2/4||||183/479|-/123|-/41|||||-1||SNV|HGNC|13930|,A|stop_gained&NMD_transcript_variant|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000488920|nonsense_mediated_decay|1/3||||293/715|121/243|41/80|E/*|Gaa/Taa|||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000503934|protein_coding||1/3|||-/560|-/419|-/139|||||-1||SNV|HGNC|13930|,A|intron_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000512418|nonsense_mediated_decay||1/5|||-/565|-/135|-/44|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000428174|protein_coding||1/2|||-/470|-/380|-/126|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000503420|protein_coding||1/3|||-/580|-/379|-/126|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000376266|protein_coding||1/17|||-/2625|-/2349|-/782|||||-1||SNV|HGNC|13930|NM_019052.3 CCHCR1 ENSG00000204536 ENST00000396268 0.01145 0.9325 0.05605 Tolerant 6 31125257 . C A 863.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.872;ClippingRankSum=0.875;DP=46;FS=11.017;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.942;POSITIVE_TRAIN_SITE;QD=18.78;ReadPosRankSum=-0.897;VQSLOD=1.29;culprit=FS;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000505392|retained_intron||1/3|||-/547|||||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000502557|protein_coding||1/3|||-/662|-/356|-/118|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000448162|protein_coding||1/4|||-/699|-/565|-/188|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000508683|protein_coding||1/4|||-/567|-/479|-/159|||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000542218|protein_coding|||||-/805|-/654|-/217||||3969|1||SNV|HGNC|11629|,A|intron_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000508852|nonsense_mediated_decay||1/4|||-/589|-/243|-/80|||||-1||SNV|HGNC|13930|,A|stop_gained|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000426967|protein_coding|1/4||||309/838|121/650|41/216|E/*|Gaa/Taa|||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000455279|protein_coding|2/5||||72/676|-/458|-/152|||||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507226|protein_coding|2/5||||44/544|-/288|-/96|||||-1||SNV|HGNC|13930|,A|stop_gained|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000451521|protein_coding|1/18||||128/2587|121/2508|41/835|E/*|Gaa/Taa|||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507829|protein_coding|2/5||||69/589|-/347|-/115|||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000376257|protein_coding|||||-/3290|-/1038|-/345||||1062|1||SNV|HGNC|11629|NM_007109.2,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000396263|protein_coding||1/15|||-/2490|-/2190|-/729|||||-1||SNV|HGNC|13930|,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000509552|retained_intron||1/13|||-/2304|||||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000464012|retained_intron|||||-/512||||||2729|-1||SNV|HGNC|13930|,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000480060|processed_transcript||1/2|||-/601|||||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000496421|processed_transcript|||||-/880||||||4004|1||SNV|HGNC|11629|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507751|protein_coding||1/3|||-/588|-/474|-/158|||||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000506831|protein_coding|1/2||||312/861|-/108|-/36|||||-1||SNV|HGNC|13930|,A|intron_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507459|nonsense_mediated_decay||1/4|||-/582|-/243|-/80|||||-1||SNV|HGNC|13930|,A|upstream_gene_variant|MODIFIER|TCF19|ENSG00000137310|Transcript|ENST00000376255|protein_coding|||||-/3039|-/1038|-/345||||1067|1||SNV|HGNC|11629|NM_001077511.1,A|stop_gained|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000396268|protein_coding|1/18||||310/2958|121/2616|41/871|E/*|Gaa/Taa|||-1|1|SNV|HGNC|13930|NM_001105563.1&NM_001105564.1,A|intron_variant&non_coding_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000475684|retained_intron||1/2|||-/786|||||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000513222|protein_coding||1/2|||-/511|-/421|-/140|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000448141|protein_coding||1/4|||-/664|-/574|-/191|||||-1||SNV|HGNC|13930|,A|5_prime_UTR_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000507892|protein_coding|2/4||||183/479|-/123|-/41|||||-1||SNV|HGNC|13930|,A|stop_gained&NMD_transcript_variant|HIGH|CCHCR1|ENSG00000204536|Transcript|ENST00000488920|nonsense_mediated_decay|1/3||||293/715|121/243|41/80|E/*|Gaa/Taa|||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000503934|protein_coding||1/3|||-/560|-/419|-/139|||||-1||SNV|HGNC|13930|,A|intron_variant&NMD_transcript_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000512418|nonsense_mediated_decay||1/5|||-/565|-/135|-/44|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000428174|protein_coding||1/2|||-/470|-/380|-/126|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000503420|protein_coding||1/3|||-/580|-/379|-/126|||||-1||SNV|HGNC|13930|,A|intron_variant|MODIFIER|CCHCR1|ENSG00000204536|Transcript|ENST00000376266|protein_coding||1/17|||-/2625|-/2349|-/782|||||-1||SNV|HGNC|13930|NM_019052.3 CCHCR1 ENSG00000204536 ENST00000488920 0.02795 0.85625 0.1158 Tolerant 6 132938842 . C T 932.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.614;ClippingRankSum=-0.869;DP=46;FS=2.652;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.498;POSITIVE_TRAIN_SITE;QD=20.28;ReadPosRankSum=1.518;VQSLOD=3.20;culprit=QD;CSQ=T|stop_gained|HIGH|TAAR2|ENSG00000146378|Transcript|ENST00000537809|protein_coding|2/2||||503/1056|368/921|123/306|W/*|tGg/tAg|||-1||SNV|HGNC|4514|NM_001033080.1,T|stop_gained|HIGH|TAAR2|ENSG00000146378|Transcript|ENST00000367931|protein_coding|2/2||||503/1056|503/1056|168/351|W/*|tGg/tAg|||-1|1|SNV|HGNC|4514|,T|stop_gained|HIGH|TAAR2|ENSG00000146378|Transcript|ENST00000275191|protein_coding|1/1||||476/1157|368/921|123/306|W/*|tGg/tAg|||-1||SNV|HGNC|4514|NM_014626.3 TAAR2 ENSG00000146378 ENST00000275191 0.0109 0.8754 0.1137 Tolerant 6 154428666 . C T 612.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.076;ClippingRankSum=0.076;DP=37;FS=4.815;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.744;POSITIVE_TRAIN_SITE;QD=16.56;ReadPosRankSum=-0.410;VQSLOD=3.39;culprit=MQRankSum;CSQ=T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000337049|protein_coding||3/3|||-/1389|-/1257|-/418|||||1||SNV|HGNC|8156|NM_001008503.1,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000452687|protein_coding||3/3|||-/1352|-/1221|-/406|||||1||SNV|HGNC|8156|NM_001145282.1,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000330432|protein_coding||3/3|||-/2178|-/1203|-/400|||||1||SNV|HGNC|8156|NM_000914.3&NM_001285524.1,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000435918|protein_coding||3/3|||-/2217|-/1194|-/397|||||1||SNV|HGNC|8156|NM_001145283.1,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000518759|protein_coding||3/3|||-/1060|-/960|-/319|||||1||SNV|HGNC|8156|NM_001145281.2,T|intron_variant&NMD_transcript_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000522739|nonsense_mediated_decay||4/4|||-/1468|-/1209|-/402|||||1||SNV|HGNC|8156|,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000414028|protein_coding||3/3|||-/2485|-/1212|-/403|||||1||SNV|HGNC|8156|NM_001145284.2,T|stop_gained|HIGH|OPRM1|ENSG00000112038|Transcript|ENST00000419506|protein_coding|4/4||||1281/1402|1231/1263|411/420|Q/*|Cag/Tag|||1||SNV|HGNC|8156|NM_001145286.1,T|intron_variant&non_coding_transcript_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000519613|processed_transcript||3/3|||-/1127|||||||1||SNV|HGNC|8156|,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000434900|protein_coding||5/5|||-/2033|-/1482|-/493|||||1|1|SNV|HGNC|8156|NM_001145279.2,T|intron_variant&NMD_transcript_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000519083|nonsense_mediated_decay||4/4|||-/2594|-/1209|-/402|||||1||SNV|HGNC|8156|,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000524163|protein_coding||3/3|||-/1251|-/1170|-/389|||||1||SNV|HGNC|8156|NM_001145285.1,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000522236|protein_coding||3/3|||-/2459|-/903|-/300|||||1||SNV|HGNC|8156|NM_001145287.1,T|intron_variant&NMD_transcript_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000524150|nonsense_mediated_decay||2/2|||-/1045|-/561|-/186|||||1||SNV|HGNC|8156|,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000520708|protein_coding||3/3|||-/1519|-/903|-/300|||||1||SNV|HGNC|8156|,T|intron_variant|MODIFIER|OPRM1|ENSG00000112038|Transcript|ENST00000522555|protein_coding||3/3|||-/2440|-/903|-/300|||||1||SNV|HGNC|8156|NM_001285526.1 OPRM1 ENSG00000112038 ENST00000419506 0.0229 0.8826 0.0945 Tolerant 6 155577717 . T A 614.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.522;ClippingRankSum=0.490;DP=42;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.490;QD=14.64;ReadPosRankSum=-0.437;VQSLOD=4.18;culprit=FS;CSQ=A|stop_gained|HIGH|TIAM2|ENSG00000146426|Transcript|ENST00000528391|protein_coding|22/22||||2742/3349|2600/3138|867/1045|L/*|tTg/tAg|||1||SNV|HGNC|11806|,A|downstream_gene_variant|MODIFIER|TFB1M|ENSG00000029639|Transcript|ENST00000470239|processed_transcript|||||-/433||||||1090|-1||SNV|HGNC|17037|,A|downstream_gene_variant|MODIFIER|TIAM2|ENSG00000146426|Transcript|ENST00000528535|protein_coding|||||-/4404|-/4101|-/1367||||4598|1||SNV|HGNC|11806|,A|downstream_gene_variant|MODIFIER|TFB1M|ENSG00000029639|Transcript|ENST00000468889|processed_transcript|||||-/621||||||1070|-1||SNV|HGNC|17037|,A|stop_gained|HIGH|TIAM2|ENSG00000146426|Transcript|ENST00000456144|protein_coding|27/27||||4863/6003|4655/5193|1552/1730|L/*|tTg/tAg|||1||SNV|HGNC|11806|,A|downstream_gene_variant|MODIFIER|TFB1M|ENSG00000029639|Transcript|ENST00000489874|processed_transcript|||||-/563||||||4240|-1||SNV|HGNC|17037|,A|stop_gained|HIGH|TIAM2|ENSG00000146426|Transcript|ENST00000367174|protein_coding|27/27||||4848/5988|2696/3234|899/1077|L/*|tTg/tAg|||1||SNV|HGNC|11806|,A|stop_gained|HIGH|TIAM2|ENSG00000146426|Transcript|ENST00000360366|protein_coding|25/25||||4692/5771|4640/5178|1547/1725|L/*|tTg/tAg|||1||SNV|HGNC|11806|,A|stop_gained|HIGH|TIAM2|ENSG00000146426|Transcript|ENST00000461783|protein_coding|29/29||||5841/6981|4568/5106|1523/1701|L/*|tTg/tAg|||1|1|SNV|HGNC|11806|,A|stop_gained|HIGH|TIAM2|ENSG00000146426|Transcript|ENST00000318981|protein_coding|26/26||||4776/5916|4568/5106|1523/1701|L/*|tTg/tAg|||1||SNV|HGNC|11806|NM_012454.3,A|stop_gained|HIGH|TIAM2|ENSG00000146426|Transcript|ENST00000275246|protein_coding|13/13||||1854/2491|1343/1881|448/626|L/*|tTg/tAg|||1||SNV|HGNC|11806|NM_001010927.2,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|RP11-477D19.2|ENSG00000235381|Transcript|ENST00000435295|antisense|1/2||||142/3088|||||||-1||SNV|Clone_based_vega_gene||,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|TIAM2|ENSG00000146426|Transcript|ENST00000537845|retained_intron|4/4||||478/581|||||||1||SNV|HGNC|11806|,A|downstream_gene_variant|MODIFIER|TFB1M|ENSG00000029639|Transcript|ENST00000495806|processed_transcript|||||-/444||||||1394|-1||SNV|HGNC|17037|,A|stop_gained|HIGH|TIAM2|ENSG00000146426|Transcript|ENST00000529824|protein_coding|25/25||||4655/5262|4655/5193|1552/1730|L/*|tTg/tAg|||1||SNV|HGNC|11806|,A|stop_gained|HIGH|TIAM2|ENSG00000146426|Transcript|ENST00000456877|protein_coding|21/21||||2658/3275|2504/3042|835/1013|L/*|tTg/tAg|||1||SNV|HGNC|11806|,A|downstream_gene_variant|MODIFIER|TFB1M|ENSG00000029639|Transcript|ENST00000367166|protein_coding|||||-/1424|-/1041|-/346||||926|-1||SNV|HGNC|17037|NM_016020.3 TIAM2 ENSG00000146426 ENST00000461783 0.1252 0.36345 0.51135 Recessive 8 52284560 . A T 593.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.993;ClippingRankSum=-0.135;DP=43;FS=1.218;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.966;POSITIVE_TRAIN_SITE;QD=13.81;ReadPosRankSum=0.086;VQSLOD=3.89;culprit=FS;CSQ=T|stop_gained|HIGH|PXDNL|ENSG00000147485|Transcript|ENST00000543296|protein_coding|19/21||||3875/4554|3774/3951|1258/1316|C/*|tgT/tgA|||-1||SNV|HGNC|26359|,T|stop_gained|HIGH|PXDNL|ENSG00000147485|Transcript|ENST00000522933|protein_coding|2/6||||995/1925|996/1614|332/537|C/*|tgT/tgA|||-1||SNV|HGNC|26359|,T|stop_gained&NMD_transcript_variant|HIGH|PXDNL|ENSG00000147485|Transcript|ENST00000522628|nonsense_mediated_decay|3/5||||1572/2258|1572/1749|524/582|C/*|tgT/tgA|||-1||SNV|HGNC|26359|,T|stop_gained|HIGH|PXDNL|ENSG00000147485|Transcript|ENST00000356297|protein_coding|19/23||||3875/4805|3774/4392|1258/1463|C/*|tgT/tgA|||-1|1|SNV|HGNC|26359|NM_144651.4 PXDNL ENSG00000147485 ENST00000356297 0.0053 0.9737 0.021 Tolerant 8 100133706 . T G 1860.77 PASS AC=2;AF=1.00;AN=2;DP=48;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.71;VQSLOD=5.66;culprit=FS;CSQ=G|intron_variant&NMD_transcript_variant|MODIFIER|VPS13B|ENSG00000132549|Transcript|ENST00000496144|nonsense_mediated_decay||8/33|||-/5625|-/4284|-/1427|||||1||SNV|HGNC|2183|,G|downstream_gene_variant|MODIFIER|CTD-2340D6.1|ENSG00000253532|Transcript|ENST00000523226|sense_intronic|||||-/595||||||897|1||SNV|Clone_based_vega_gene||,G|intron_variant|MODIFIER|VPS13B|ENSG00000132549|Transcript|ENST00000357162|protein_coding||8/61|||-/14019|-/11994|-/3997|||||1||SNV|HGNC|2183|NM_152564.4,G|intron_variant|MODIFIER|VPS13B|ENSG00000132549|Transcript|ENST00000355155|protein_coding||8/17|||-/2822|-/2592|-/863|||||1||SNV|HGNC|2183|NM_015243.2,G|stop_gained|HIGH|VPS13B|ENSG00000132549|Transcript|ENST00000441350|protein_coding|8/8||||1342/1626|1239/1248|413/415|Y/*|taT/taG|||1||SNV|HGNC|2183|NM_181661.2,G|downstream_gene_variant|MODIFIER|VPS13B|ENSG00000132549|Transcript|ENST00000524330|processed_transcript|||||-/218||||||146|1||SNV|HGNC|2183|,G|intron_variant|MODIFIER|VPS13B|ENSG00000132549|Transcript|ENST00000358544|protein_coding||8/61|||-/14094|-/12069|-/4022|||||1|1|SNV|HGNC|2183|NM_017890.4,G|intron_variant|MODIFIER|VPS13B|ENSG00000132549|Transcript|ENST00000395996|protein_coding||8/62|||-/14160|-/4284|-/1427|||||1||SNV|HGNC|2183| VPS13B ENSG00000132549 ENST00000441350 0.0247 0.90805 0.06725 Tolerant 9 134385435 . C T 507.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.074;ClippingRankSum=-1.557;DP=29;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.899;POSITIVE_TRAIN_SITE;QD=17.51;ReadPosRankSum=2.083;VQSLOD=5.67;culprit=FS;CSQ=T|intron_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000419118|protein_coding||5/16|||-/2189|-/1722|-/573|||||1||SNV|HGNC|9202|,T|upstream_gene_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000485278|processed_transcript|||||-/3420||||||452|1||SNV|HGNC|9202|,T|intron_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000415075|protein_coding||5/7|||-/847|-/470|-/156|||||1||SNV|HGNC|9202|,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000462375|processed_transcript|3/6||||309/1001|||||||1||SNV|HGNC|9202|,T|stop_gained|HIGH|POMT1|ENSG00000130714|Transcript|ENST00000372228|protein_coding|8/20||||930/3123|751/2244|251/747|Q/*|Cag/Tag|||1|1|SNV|HGNC|9202|NM_007171.3,T|intron_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000541219|protein_coding||2/12|||-/1587|-/1398|-/465|||||1||SNV|HGNC|9202|,T|stop_gained|HIGH|POMT1|ENSG00000130714|Transcript|ENST00000441334|protein_coding|6/10||||678/1168|400/890|134/296|Q/*|Cag/Tag|||1||SNV|HGNC|9202|,T|intron_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000404875|protein_coding||6/17|||-/2821|-/1827|-/608|||||1||SNV|HGNC|9202|NM_001136114.1,T|stop_gained|HIGH|POMT1|ENSG00000130714|Transcript|ENST00000448212|protein_coding|7/8||||725/791|589/655|197/218|Q/*|Cag/Tag|||1||SNV|HGNC|9202|,T|downstream_gene_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000418774|protein_coding|||||-/812|-/427|-/142||||2534|1||SNV|HGNC|9202|,T|intron_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000354713|protein_coding||7/18|||-/2573|-/2088|-/695|||||1||SNV|HGNC|9202|,T|intron_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000341012|protein_coding||7/18|||-/2912|-/2016|-/671|||||1||SNV|HGNC|9202|NM_001077366.1,T|downstream_gene_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000483472|processed_transcript|||||-/568||||||3275|1||SNV|HGNC|9202|,T|intron_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000430619|protein_coding||6/6|||-/691|-/504|-/168|||||1||SNV|HGNC|9202|,T|intron_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000402686|protein_coding||8/19|||-/3038|-/2178|-/725|||||1||SNV|HGNC|9202|NM_001077365.1,T|intron_variant|MODIFIER|POMT1|ENSG00000130714|Transcript|ENST00000423007|protein_coding||8/19|||-/3320|-/2178|-/725|||||1||SNV|HGNC|9202|NM_001136113.1 POMT1 ENSG00000130714 ENST00000372228 0.00875 0.93635 0.0549 Tolerant 9 136029645 . G T 1391.77 PASS AC=2;AF=1.00;AN=2;DP=37;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=30.10;VQSLOD=5.57;culprit=FS;CSQ=T|stop_gained|HIGH|GBGT1|ENSG00000148288|Transcript|ENST00000372040|protein_coding|7/7||||675/1980|363/1044|121/347|Y/*|taC/taA|||-1|1|SNV|HGNC|20460|,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|GBGT1|ENSG00000148288|Transcript|ENST00000470431|processed_transcript|6/6||||1565/2870|||||||-1||SNV|HGNC|20460|,T|missense_variant|MODERATE|GBGT1|ENSG00000148288|Transcript|ENST00000372038|protein_coding|7/7||||664/847|400/483|134/160|H/N|Cac/Aac|||-1||SNV|HGNC|20460|,T|stop_gained|HIGH|GBGT1|ENSG00000148288|Transcript|ENST00000540636|protein_coding|6/6||||593/1449|312/993|104/330|Y/*|taC/taA|||-1||SNV|HGNC|20460|NM_001282632.1,T|upstream_gene_variant|MODIFIER|RALGDS|ENSG00000160271|Transcript|ENST00000393160|protein_coding|||||-/3801|-/2580|-/859||||4924|-1||SNV|HGNC|9842|NM_001042368.2,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|GBGT1|ENSG00000148288|Transcript|ENST00000472281|processed_transcript|5/5||||1643/2948|||||||-1||SNV|HGNC|20460|,T|intron_variant|MODIFIER|RALGDS|ENSG00000160271|Transcript|ENST00000542690|protein_coding||6/22|||-/3705|-/2958|-/985|||||-1||SNV|HGNC|9842|,T|intron_variant|MODIFIER|GBGT1|ENSG00000148288|Transcript|ENST00000372043|protein_coding||6/6|||-/1935|-/885|-/294|||||-1||SNV|HGNC|20460|NM_021996.4&NM_001282629.1 GBGT1 ENSG00000148288 ENST00000372040 0.00265 0.94775 0.0496 Tolerant 9 139937799 . G A 1459.77 PASS AC=2;AF=1.00;AN=2;DP=33;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.05;VQSLOD=5.24;culprit=FS;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|NPDC1|ENSG00000107281|Transcript|ENST00000485589|processed_transcript||1/1|||-/506|||||||-1||SNV|HGNC|7899|,A|downstream_gene_variant|MODIFIER|ENTPD2|ENSG00000054179|Transcript|ENST00000355097|protein_coding|||||-/2095|-/1488|-/495||||4751|-1||SNV|HGNC|3364|NM_001246.3&NM_203468.2,A|intron_variant|MODIFIER|NPDC1|ENSG00000107281|Transcript|ENST00000371601|protein_coding||1/8|||-/1494|-/978|-/325|||||-1|1|SNV|HGNC|7899|NM_015392.3,A|stop_gained|HIGH|NPDC1|ENSG00000107281|Transcript|ENST00000371600|protein_coding|1/8||||746/2187|73/1212|25/403|R/*|Cga/Tga|||-1||SNV|HGNC|7899|,A|upstream_gene_variant|MODIFIER|NPDC1|ENSG00000107281|Transcript|ENST00000496498|processed_transcript|||||-/383||||||3191|-1||SNV|HGNC|7899|,A|upstream_gene_variant|MODIFIER|NPDC1|ENSG00000107281|Transcript|ENST00000472668|processed_transcript|||||-/358||||||2969|-1||SNV|HGNC|7899|,A|downstream_gene_variant|MODIFIER|ENTPD2|ENSG00000054179|Transcript|ENST00000460614|processed_transcript|||||-/1427||||||4760|-1||SNV|HGNC|3364|,A|intron_variant&non_coding_transcript_variant|MODIFIER|NPDC1|ENSG00000107281|Transcript|ENST00000488145|processed_transcript||1/2|||-/701|||||||-1||SNV|HGNC|7899| NPDC1 ENSG00000107281 ENST00000371600 0.105 0.6205 0.2745 Tolerant 10 4889403 . C T 635.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.628;ClippingRankSum=0.106;DP=40;FS=1.289;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.167;POSITIVE_TRAIN_SITE;QD=15.89;ReadPosRankSum=0.927;VQSLOD=4.68;culprit=MQRankSum;CSQ=T|3_prime_UTR_variant|MODIFIER|AKR1E2|ENSG00000165568|Transcript|ENST00000487985|protein_coding|4/4||||247/381|-/171|-/56|||||1||SNV|HGNC|23437|,T|stop_gained|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000345253|protein_coding|6/7||||636/913|607/669|203/222|R/*|Cga/Tga|||1||SNV|HGNC|23437|NM_001271025.1,T|stop_gained|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000334019|protein_coding|7/8||||759/1036|730/792|244/263|R/*|Cga/Tga|||1||SNV|HGNC|23437|NM_001271021.1,T|downstream_gene_variant|MODIFIER|AKR1E2|ENSG00000165568|Transcript|ENST00000525281|processed_transcript|||||-/1041||||||1012|1||SNV|HGNC|23437|,T|stop_gained|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000532248|protein_coding|7/7||||759/844|730/753|244/250|R/*|Cga/Tga|||1||SNV|HGNC|23437|,T|downstream_gene_variant|MODIFIER|AKR1E2|ENSG00000165568|Transcript|ENST00000441590|processed_transcript|||||-/488||||||1400|1||SNV|HGNC|23437|,T|stop_gained&NMD_transcript_variant|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000463345|nonsense_mediated_decay|9/10||||992/1655|901/924|301/307|R/*|Cga/Tga|||1||SNV|HGNC|23437|,T|stop_gained|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000298375|protein_coding|9/10||||972/1566|901/963|301/320|R/*|Cga/Tga|||1|1|SNV|HGNC|23437|NM_001040177.2,T|stop_gained&NMD_transcript_variant|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000474119|nonsense_mediated_decay|9/10||||963/1626|589/612|197/203|R/*|Cga/Tga|||1||SNV|HGNC|23437| AKR1E2 ENSG00000165568 ENST00000463345 0.00405 0.90555 0.0904 Tolerant 10 4889403 . C T 635.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.628;ClippingRankSum=0.106;DP=40;FS=1.289;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.167;POSITIVE_TRAIN_SITE;QD=15.89;ReadPosRankSum=0.927;VQSLOD=4.68;culprit=MQRankSum;CSQ=T|3_prime_UTR_variant|MODIFIER|AKR1E2|ENSG00000165568|Transcript|ENST00000487985|protein_coding|4/4||||247/381|-/171|-/56|||||1||SNV|HGNC|23437|,T|stop_gained|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000345253|protein_coding|6/7||||636/913|607/669|203/222|R/*|Cga/Tga|||1||SNV|HGNC|23437|NM_001271025.1,T|stop_gained|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000334019|protein_coding|7/8||||759/1036|730/792|244/263|R/*|Cga/Tga|||1||SNV|HGNC|23437|NM_001271021.1,T|downstream_gene_variant|MODIFIER|AKR1E2|ENSG00000165568|Transcript|ENST00000525281|processed_transcript|||||-/1041||||||1012|1||SNV|HGNC|23437|,T|stop_gained|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000532248|protein_coding|7/7||||759/844|730/753|244/250|R/*|Cga/Tga|||1||SNV|HGNC|23437|,T|downstream_gene_variant|MODIFIER|AKR1E2|ENSG00000165568|Transcript|ENST00000441590|processed_transcript|||||-/488||||||1400|1||SNV|HGNC|23437|,T|stop_gained&NMD_transcript_variant|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000463345|nonsense_mediated_decay|9/10||||992/1655|901/924|301/307|R/*|Cga/Tga|||1||SNV|HGNC|23437|,T|stop_gained|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000298375|protein_coding|9/10||||972/1566|901/963|301/320|R/*|Cga/Tga|||1|1|SNV|HGNC|23437|NM_001040177.2,T|stop_gained&NMD_transcript_variant|HIGH|AKR1E2|ENSG00000165568|Transcript|ENST00000474119|nonsense_mediated_decay|9/10||||963/1626|589/612|197/203|R/*|Cga/Tga|||1||SNV|HGNC|23437| AKR1E2 ENSG00000165568 ENST00000298375 0.00235 0.9471 0.05055 Tolerant 11 5068662 . C T 760.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.564;ClippingRankSum=-0.381;DP=38;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.594;POSITIVE_TRAIN_SITE;QD=20.02;ReadPosRankSum=0.594;VQSLOD=4.74;culprit=FS;CSQ=T|stop_gained|HIGH|OR52J3|ENSG00000205495|Transcript|ENST00000380370|protein_coding|1/1||||907/936|907/936|303/311|R/*|Cga/Tga|||1|1|SNV|HGNC|14799|NM_001001916.2 OR52J3 ENSG00000205495 ENST00000380370 0.0011 0.9928 0.0061 Tolerant 11 5776484 . A T 974.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.663;ClippingRankSum=-0.699;DP=44;FS=6.422;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.747;POSITIVE_TRAIN_SITE;QD=22.15;ReadPosRankSum=1.181;VQSLOD=1.83;culprit=QD;CSQ=T|intron_variant|MODIFIER|TRIM5|ENSG00000132256|Transcript|ENST00000412903|protein_coding||2/4|||-/1054|-/628|-/209|||||-1||SNV|HGNC|16276|,T|intron_variant|MODIFIER|TRIM5|ENSG00000132256|Transcript|ENST00000380027|protein_coding||3/10|||-/2290|-/981|-/326|||||-1||SNV|HGNC|16276|,T|stop_gained|HIGH|OR52N4|ENSG00000181074|Transcript|ENST00000317254|protein_coding|1/1||||562/1037|514/966|172/321|R/*|Aga/Tga|||1|1|SNV|HGNC|15230|NM_001005175.3 OR52N4 ENSG00000181074 ENST00000317254 0.0018 0.98925 0.00895 Tolerant 11 7712471 . C T 676.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.934;ClippingRankSum=-1.187;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.769;POSITIVE_TRAIN_SITE;QD=16.51;ReadPosRankSum=0.978;VQSLOD=5.58;culprit=FS;CSQ=T|intron_variant|MODIFIER|OVCH2|ENSG00000183378|Transcript|ENST00000534193|polymorphic_pseudogene||15/16|||-/1765|-/1750|-/583|||||-1||SNV|HGNC|29970|,T|stop_gained|HIGH|OVCH2|ENSG00000183378|Transcript|ENST00000454689|protein_coding|15/15||||1668/1695|1668/1695|556/564|W/*|tgG/tgA|||-1|1|SNV|HGNC|29970|NM_198185.3,T|intron_variant&non_coding_transcript_variant|MODIFIER|OVCH2|ENSG00000183378|Transcript|ENST00000533663|processed_transcript||3/4|||-/613|||||||-1||SNV|HGNC|29970| OVCH2 ENSG00000183378 ENST00000454689 7e-04 0.99375 0.00555 Tolerant 11 33106616 . C T 507.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.185;ClippingRankSum=0.100;DP=39;FS=4.662;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.357;POSITIVE_TRAIN_SITE;QD=13.02;ReadPosRankSum=0.671;VQSLOD=3.71;culprit=MQRankSum;CSQ=T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|CSTF3|ENSG00000176102|Transcript|ENST00000528865|nonsense_mediated_decay|3/4||||291/592|-/276|-/91|||||-1||SNV|HGNC|2485|,T|stop_gained&NMD_transcript_variant|HIGH|TCP11L1|ENSG00000176148|Transcript|ENST00000527661|nonsense_mediated_decay|12/13||||1983/2468|1738/1788|580/595|Q/*|Cag/Tag|||1||SNV|HGNC|25655|,T|3_prime_UTR_variant|MODIFIER|CSTF3|ENSG00000176102|Transcript|ENST00000323959|protein_coding|21/21||||2311/2797|-/2154|-/717|||||-1|1|SNV|HGNC|2485|NM_001326.2,T|intron_variant|MODIFIER|TCP11L1|ENSG00000176148|Transcript|ENST00000528962|protein_coding||2/2|||-/711|-/477|-/158|||||1||SNV|HGNC|25655|,T|stop_gained|HIGH|TCP11L1|ENSG00000176148|Transcript|ENST00000324357|protein_coding|7/8||||1087/1572|1075/1125|359/374|Q/*|Cag/Tag|||1||SNV|HGNC|25655| TCP11L1 ENSG00000176148 ENST00000527661 0.00485 0.96185 0.0333 Tolerant 11 33106616 . C T 507.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.185;ClippingRankSum=0.100;DP=39;FS=4.662;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.357;POSITIVE_TRAIN_SITE;QD=13.02;ReadPosRankSum=0.671;VQSLOD=3.71;culprit=MQRankSum;CSQ=T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|CSTF3|ENSG00000176102|Transcript|ENST00000528865|nonsense_mediated_decay|3/4||||291/592|-/276|-/91|||||-1||SNV|HGNC|2485|,T|stop_gained&NMD_transcript_variant|HIGH|TCP11L1|ENSG00000176148|Transcript|ENST00000527661|nonsense_mediated_decay|12/13||||1983/2468|1738/1788|580/595|Q/*|Cag/Tag|||1||SNV|HGNC|25655|,T|3_prime_UTR_variant|MODIFIER|CSTF3|ENSG00000176102|Transcript|ENST00000323959|protein_coding|21/21||||2311/2797|-/2154|-/717|||||-1|1|SNV|HGNC|2485|NM_001326.2,T|intron_variant|MODIFIER|TCP11L1|ENSG00000176148|Transcript|ENST00000528962|protein_coding||2/2|||-/711|-/477|-/158|||||1||SNV|HGNC|25655|,T|stop_gained|HIGH|TCP11L1|ENSG00000176148|Transcript|ENST00000324357|protein_coding|7/8||||1087/1572|1075/1125|359/374|Q/*|Cag/Tag|||1||SNV|HGNC|25655| TCP11L1 ENSG00000176148 ENST00000324357 0.0129 0.89185 0.09525 Tolerant 11 56431216 . C T 694.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=3.523;ClippingRankSum=0.219;DP=39;FS=1.279;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.190;POSITIVE_TRAIN_SITE;QD=17.81;ReadPosRankSum=-0.570;VQSLOD=4.36;culprit=QD;CSQ=T|stop_gained|HIGH|OR5AR1|ENSG00000172459|Transcript|ENST00000302969|protein_coding|1/1||||79/1026|55/933|19/310|Q/*|Cag/Tag|||1|1|SNV|HGNC|15260|NM_001004730.1 OR5AR1 ENSG00000172459 ENST00000302969 0.0025 0.97055 0.02695 Tolerant 11 62369881 . G A 334.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.602;ClippingRankSum=0.968;DP=36;FS=1.407;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.091;POSITIVE_TRAIN_SITE;QD=9.30;ReadPosRankSum=0.456;VQSLOD=4.54;culprit=FS;CSQ=A|3_prime_UTR_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000278845|protein_coding|22/22||||2827/3017|-/2694|-/897|||||-1||SNV|HGNC|26666|,A|upstream_gene_variant|MODIFIER|MTA2|ENSG00000149480|Transcript|ENST00000524902|protein_coding|||||-/2577|-/1488|-/495||||3092|-1||SNV|HGNC|7411|,A|upstream_gene_variant|MODIFIER|MTA2|ENSG00000149480|Transcript|ENST00000527204|protein_coding|||||-/2265|-/1488|-/495||||1134|-1||SNV|HGNC|7411|,A|stop_gained|HIGH|EML3|ENSG00000149499|Transcript|ENST00000494176|protein_coding|21/21||||2712/2901|2563/2670|855/889|Q/*|Caa/Taa|||-1||SNV|HGNC|26666|,A|upstream_gene_variant|MODIFIER|MTA2|ENSG00000149480|Transcript|ENST00000531261|retained_intron|||||-/563||||||4280|-1||SNV|HGNC|7411|,A|upstream_gene_variant|MODIFIER|MTA2|ENSG00000149480|Transcript|ENST00000278823|protein_coding|||||-/3058|-/2007|-/668||||569|-1||SNV|HGNC|7411|NM_004739.3,A|upstream_gene_variant|MODIFIER|RP11-831H9.3|ENSG00000254964|Transcript|ENST00000532626|antisense|||||-/92||||||3752|1||SNV|Clone_based_vega_gene||,A|3_prime_UTR_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000394773|protein_coding|22/22||||3065/3256|-/2691|-/896|||||-1|1|SNV|HGNC|26666|NM_153265.2,A|downstream_gene_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000438258|processed_transcript|||||-/493||||||3501|-1||SNV|HGNC|26666|,A|stop_gained|HIGH|EML3|ENSG00000149499|Transcript|ENST00000529309|protein_coding|22/22||||2720/2909|2647/2754|883/917|Q/*|Caa/Taa|||-1||SNV|HGNC|26666|,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000460939|retained_intron|8/8||||1581/1770|||||||-1||SNV|HGNC|26666|,A|stop_gained|HIGH|EML3|ENSG00000149499|Transcript|ENST00000394776|protein_coding|21/21||||2628/2818|2629/2736|877/911|Q/*|Caa/Taa|||-1||SNV|HGNC|26666|,A|downstream_gene_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000526116|retained_intron|||||-/581||||||3187|-1||SNV|HGNC|26666|,A|downstream_gene_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000462626|retained_intron|||||-/463||||||3428|-1||SNV|HGNC|26666|,A|downstream_gene_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000483199|retained_intron|||||-/1042||||||1664|-1||SNV|HGNC|26666|,A|3_prime_UTR_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000439994|protein_coding|3/3||||480/671|-/414|-/137|||||-1||SNV|HGNC|26666|,A|downstream_gene_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000533165|retained_intron|||||-/524||||||707|-1||SNV|HGNC|26666|,A|upstream_gene_variant|MODIFIER|MTA2|ENSG00000149480|Transcript|ENST00000532239|retained_intron|||||-/532||||||2063|-1||SNV|HGNC|7411|,A|downstream_gene_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000524518|retained_intron|||||-/514||||||2299|-1||SNV|HGNC|26666|,A|upstream_gene_variant|MODIFIER|MTA2|ENSG00000149480|Transcript|ENST00000526844|retained_intron|||||-/627||||||922|-1||SNV|HGNC|7411|,A|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000494448|nonsense_mediated_decay|21/21||||3482/3665|-/585|-/194|||||-1||SNV|HGNC|26666|,A|3_prime_UTR_variant|MODIFIER|EML3|ENSG00000149499|Transcript|ENST00000531557|protein_coding|19/19||||2320/2509|-/2040|-/679|||||-1||SNV|HGNC|26666| EML3 ENSG00000149499 ENST00000529309 0.02975 0.8852 0.08505 Tolerant 11 62848487 . A C 658.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-3.028;ClippingRankSum=-0.662;DP=39;FS=1.252;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.127;POSITIVE_TRAIN_SITE;QD=16.89;ReadPosRankSum=-0.352;VQSLOD=4.52;culprit=MQRankSum;CSQ=C|stop_gained|HIGH|SLC22A24|ENSG00000197658|Transcript|ENST00000417740|protein_coding|9/10||||1945/2098|1503/1656|501/551|Y/*|taT/taG|||-1|1|SNV|HGNC|28542|NM_001136506.2 SLC22A24 ENSG00000197658 ENST00000417740 0.0047 0.97575 0.01955 Tolerant 11 63057925 . G A 683.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;ClippingRankSum=-0.383;DP=37;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.650;POSITIVE_TRAIN_SITE;QD=18.48;ReadPosRankSum=0.350;VQSLOD=5.67;culprit=FS;CSQ=A|5_prime_UTR_variant|MODIFIER|SLC22A10|ENSG00000184999|Transcript|ENST00000544661|protein_coding|2/11||||251/2181|-/810|-/269|||||1||SNV|HGNC|18057|,A|intron_variant|MODIFIER|SLC22A10|ENSG00000184999|Transcript|ENST00000535888|protein_coding||4/9|||-/1200|-/444|-/147|||||1||SNV|HGNC|18057|,A|intron_variant&non_coding_transcript_variant|MODIFIER|SLC22A10|ENSG00000184999|Transcript|ENST00000525620|processed_transcript||5/10|||-/1205|||||||1||SNV|HGNC|18057|,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|SLC22A10|ENSG00000184999|Transcript|ENST00000533176|processed_transcript|1/2||||362/559|||||||1||SNV|HGNC|18057|,A|stop_gained&NMD_transcript_variant|HIGH|SLC22A10|ENSG00000184999|Transcript|ENST00000532724|nonsense_mediated_decay|1/7||||155/864|132/795|44/264|W/*|tgG/tgA|||1||SNV|HGNC|18057|,A|stop_gained&NMD_transcript_variant|HIGH|SLC22A10|ENSG00000184999|Transcript|ENST00000533483|nonsense_mediated_decay|2/11||||298/2234|132/1119|44/372|W/*|tgG/tgA|||1||SNV|HGNC|18057|,A|stop_gained|HIGH|SLC22A10|ENSG00000184999|Transcript|ENST00000332793|protein_coding|1/10||||290/2026|288/1626|96/541|W/*|tgG/tgA|||1|1|SNV|HGNC|18057|NM_001039752.3,A|stop_gained|HIGH|SLC22A10|ENSG00000184999|Transcript|ENST00000526800|protein_coding|1/5||||146/699|132/618|44/205|W/*|tgG/tgA|||1||SNV|HGNC|18057| SLC22A10 ENSG00000184999 ENST00000533483 0.00355 0.91675 0.0797 Tolerant 11 63057925 . G A 683.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.317;ClippingRankSum=-0.383;DP=37;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.650;POSITIVE_TRAIN_SITE;QD=18.48;ReadPosRankSum=0.350;VQSLOD=5.67;culprit=FS;CSQ=A|5_prime_UTR_variant|MODIFIER|SLC22A10|ENSG00000184999|Transcript|ENST00000544661|protein_coding|2/11||||251/2181|-/810|-/269|||||1||SNV|HGNC|18057|,A|intron_variant|MODIFIER|SLC22A10|ENSG00000184999|Transcript|ENST00000535888|protein_coding||4/9|||-/1200|-/444|-/147|||||1||SNV|HGNC|18057|,A|intron_variant&non_coding_transcript_variant|MODIFIER|SLC22A10|ENSG00000184999|Transcript|ENST00000525620|processed_transcript||5/10|||-/1205|||||||1||SNV|HGNC|18057|,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|SLC22A10|ENSG00000184999|Transcript|ENST00000533176|processed_transcript|1/2||||362/559|||||||1||SNV|HGNC|18057|,A|stop_gained&NMD_transcript_variant|HIGH|SLC22A10|ENSG00000184999|Transcript|ENST00000532724|nonsense_mediated_decay|1/7||||155/864|132/795|44/264|W/*|tgG/tgA|||1||SNV|HGNC|18057|,A|stop_gained&NMD_transcript_variant|HIGH|SLC22A10|ENSG00000184999|Transcript|ENST00000533483|nonsense_mediated_decay|2/11||||298/2234|132/1119|44/372|W/*|tgG/tgA|||1||SNV|HGNC|18057|,A|stop_gained|HIGH|SLC22A10|ENSG00000184999|Transcript|ENST00000332793|protein_coding|1/10||||290/2026|288/1626|96/541|W/*|tgG/tgA|||1|1|SNV|HGNC|18057|NM_001039752.3,A|stop_gained|HIGH|SLC22A10|ENSG00000184999|Transcript|ENST00000526800|protein_coding|1/5||||146/699|132/618|44/205|W/*|tgG/tgA|||1||SNV|HGNC|18057| SLC22A10 ENSG00000184999 ENST00000332793 0.00145 0.98265 0.0159 Tolerant 11 76751587 . G A 595.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388;ClippingRankSum=0.144;DP=52;FS=4.096;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.220;QD=11.46;ReadPosRankSum=1.388;VQSLOD=2.03;culprit=QD;CSQ=A|coding_sequence_variant|MODIFIER|B3GNT6|ENSG00000198488|Transcript|ENST00000421061|protein_coding||5/5|||-/792|-/792|-/263|||||1||SNV|HGNC|24141|,A|missense_variant|MODERATE|B3GNT6|ENSG00000198488|Transcript|ENST00000533140|protein_coding|2/2||||1130/2639|992/1158|331/385|G/D|gGc/gAc|||1|1|SNV|HGNC|24141|NM_138706.4,A|stop_gained&splice_region_variant|HIGH|B3GNT6|ENSG00000198488|Transcript|ENST00000354301|protein_coding|4/5||||1078/2493|990/1155|330/384|W/*|tgG/tgA|||1||SNV|HGNC|24141|,A|downstream_gene_variant|MODIFIER|B3GNT6|ENSG00000198488|Transcript|ENST00000528622|protein_coding|||||-/568|-/364|-/121||||628|1||SNV|HGNC|24141| B3GNT6 ENSG00000198488 ENST00000354301 0.0665 0.67305 0.26045 Tolerant 11 104763117 . G A 1546.77 PASS AC=2;AF=1.00;AN=2;DP=41;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=32.31;VQSLOD=5.86;culprit=FS;CSQ=A|synonymous_variant&NMD_transcript_variant|LOW|CASP12|ENSG00000204403|Transcript|ENST00000417998|nonsense_mediated_decay|4/8||||724/1401|468/507|156/168|C|tgC/tgT|||-1||SNV|HGNC|19004|,A|stop_gained|HIGH|CASP12|ENSG00000204403|Transcript|ENST00000375726|protein_coding|3/7||||629/1306|373/1026|125/341|R/*|Cga/Tga|||-1||SNV|HGNC|19004|,A|stop_gained|HIGH|CASP12|ENSG00000204403|Transcript|ENST00000446862|protein_coding|3/6||||629/1196|373/834|125/277|R/*|Cga/Tga|||-1||SNV|HGNC|19004|,A|stop_gained|HIGH|CASP12|ENSG00000204403|Transcript|ENST00000508062|protein_coding|2/6||||121/774|121/774|41/257|R/*|Cga/Tga|||-1||SNV|HGNC|19004|,A|stop_gained|HIGH|CASP12|ENSG00000204403|Transcript|ENST00000441710|protein_coding|3/6||||629/1168|373/888|125/295|R/*|Cga/Tga|||-1||SNV|HGNC|19004|,A|stop_gained|HIGH|CASP12|ENSG00000204403|Transcript|ENST00000494737|protein_coding|3/5||||629/961|373/681|125/226|R/*|Cga/Tga|||-1||SNV|HGNC|19004|,A|stop_gained|HIGH|CASP12|ENSG00000204403|Transcript|ENST00000448103|protein_coding|3/6||||629/1071|373/675|125/224|R/*|Cga/Tga|||-1||SNV|HGNC|19004|,A|synonymous_variant&NMD_transcript_variant|LOW|CASP12|ENSG00000204403|Transcript|ENST00000458137|nonsense_mediated_decay|4/7||||724/1166|468/507|156/168|C|tgC/tgT|||-1||SNV|HGNC|19004|,A|stop_gained|HIGH|CASP12|ENSG00000204403|Transcript|ENST00000433738|protein_coding|2/4||||377/709|121/429|41/142|R/*|Cga/Tga|||-1||SNV|HGNC|19004|,A|stop_gained|HIGH|CASP12|ENSG00000204403|Transcript|ENST00000422698|protein_coding|3/8||||392/1451|373/1026|125/341|R/*|Cga/Tga|||-1|1|SNV|HGNC|19004|NM_001191016.1,A|stop_gained|HIGH|CASP12|ENSG00000204403|Transcript|ENST00000447913|protein_coding|2/5||||377/819|121/423|41/140|R/*|Cga/Tga|||-1||SNV|HGNC|19004| CASP12 ENSG00000204403 ENST00000422698 0.024 0.82525 0.15075 Tolerant 11 124056732 . T G 302.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.194;ClippingRankSum=-0.156;DP=26;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.052;POSITIVE_TRAIN_SITE;QD=11.64;ReadPosRankSum=0.986;VQSLOD=6.22;culprit=FS;CSQ=G|stop_gained|HIGH|OR10D3|ENSG00000197309|Transcript|ENST00000318666|protein_coding|1/1||||810/1030|756/939|252/312|Y/*|taT/taG|||1|1|SNV|HGNC|8168| OR10D3 ENSG00000197309 ENST00000318666 0.0047 0.94715 0.04815 Tolerant 12 40834955 . C A 831.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.258;ClippingRankSum=0.013;DP=42;FS=4.770;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.572;POSITIVE_TRAIN_SITE;QD=19.80;ReadPosRankSum=-1.334;VQSLOD=2.86;culprit=QD;CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-115F18.1|ENSG00000258167|Transcript|ENST00000552757|antisense||1/3|||-/356|||||||-1||SNV|Clone_based_vega_gene||,A|stop_gained|HIGH|MUC19|ENSG00000205592|Transcript|ENST00000454784|protein_coding|24/84||||2695/19628|1962/10893|654/3630|C/*|tgC/tgA|||1|1|SNV|HGNC|14362|,A|3_prime_UTR_variant|MODIFIER|MUC19|ENSG00000205592|Transcript|ENST00000425730|protein_coding|24/47||||2695/4965|-/618|-/205|||||1||SNV|HGNC|14362| MUC19 ENSG00000205592 ENST00000454784 0.0269 0.7718 0.2013 Tolerant 12 55641255 . C T 1432.77 PASS AC=2;AF=1.00;AN=2;DP=36;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=25.86;VQSLOD=5.31;culprit=FS;CSQ=T|stop_gained|HIGH|OR6C74|ENSG00000197706|Transcript|ENST00000343870|protein_coding|1/1||||274/1105|184/939|62/312|R/*|Cga/Tga|||1|1|SNV|HGNC|31303|NM_001005490.1 OR6C74 ENSG00000197706 ENST00000343870 0.00065 0.9881 0.01125 Tolerant 14 92537223 . G T 616.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.740;ClippingRankSum=0.014;DP=39;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.351;POSITIVE_TRAIN_SITE;QD=15.81;ReadPosRankSum=1.503;VQSLOD=5.47;culprit=FS;CSQ=T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556374|nonsense_mediated_decay|||||-/1083|-/345|-/114||||59|-1||SNV|HGNC|7106|,T|intron_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000545170|protein_coding||10/10|||-/6950|-/1113|-/370|||||-1||SNV|HGNC|7106|NM_004993.5&NM_001164776.1&NM_001164778.1&NM_001164774.1&NM_001164777.1,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556288|nonsense_mediated_decay|||||-/901|-/240|-/79||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000557311|protein_coding|||||-/562|-/454|-/151||||56|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556644|processed_transcript|||||-/372||||||59|-1||SNV|HGNC|7106|,T|intron_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000429774|protein_coding||10/10|||-/6902|-/1065|-/354|||||-1||SNV|HGNC|7106|NM_001127696.1&NM_001164779.1&NM_001164782.1,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556220|protein_coding|||||-/692|-/670|-/223||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000554994|nonsense_mediated_decay|||||-/922|-/453|-/150||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000554592|protein_coding|||||-/1010|-/988|-/329||||56|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000553491|protein_coding|||||-/857|-/835|-/278||||59|-1||SNV|HGNC|7106|NM_001127697.2,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000557030|nonsense_mediated_decay|||||-/807|-/603|-/200||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000555381|protein_coding|||||-/803|-/781|-/260||||56|-1||SNV|HGNC|7106|NM_001164781.1,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556898|nonsense_mediated_decay|||||-/990|-/480|-/159||||56|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000553686|processed_transcript|||||-/869||||||59|-1||SNV|HGNC|7106|,T|intron_variant&NMD_transcript_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000359366|nonsense_mediated_decay||9/9|||-/2584|-/240|-/79|||||-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000554040|processed_transcript|||||-/592||||||59|-1||SNV|HGNC|7106|,T|intron_variant&non_coding_transcript_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000526245|processed_transcript||2/2|||-/352|||||||-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000555816|nonsense_mediated_decay|||||-/760|-/240|-/79||||56|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556082|nonsense_mediated_decay|||||-/660|-/240|-/79||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000553570|nonsense_mediated_decay|||||-/757|-/288|-/95||||59|-1||SNV|HGNC|7106|,T|intron_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000340660|protein_coding||9/9|||-/1205|-/921|-/306|||||-1||SNV|HGNC|7106|NM_030660.4,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000553488|nonsense_mediated_decay|||||-/1065|-/240|-/79||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000553309|processed_transcript|||||-/1022||||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556274|nonsense_mediated_decay|||||-/913|-/240|-/79||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000554672|protein_coding|||||-/759|-/697|-/232||||56|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000555958|processed_transcript|||||-/857||||||59|-1||SNV|HGNC|7106|,T|intron_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000393287|protein_coding||10/10|||-/4713|-/1086|-/361|||||-1|1|SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556671|nonsense_mediated_decay|||||-/921|-/333|-/110||||59|-1||SNV|HGNC|7106|,T|intron_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000503767|protein_coding||9/9|||-/1315|-/1041|-/346|||||-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000554214|processed_transcript|||||-/771||||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556315|nonsense_mediated_decay|||||-/924|-/237|-/78||||56|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556339|processed_transcript|||||-/525||||||59|-1||SNV|HGNC|7106|,T|stop_gained|HIGH|ATXN3|ENSG00000066427|Transcript|ENST00000532032|protein_coding|10/10||||1057/1191|1047/1095|349/364|Y/*|taC/taA|||-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000554491|processed_transcript|||||-/1064||||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000553498|processed_transcript|||||-/911||||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000556958|nonsense_mediated_decay|||||-/769|-/300|-/99||||59|-1||SNV|HGNC|7106|,T|intron_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000502250|protein_coding||7/7|||-/1259|-/549|-/182|||||-1||SNV|HGNC|7106|NM_001164780.1,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000553287|processed_transcript|||||-/726||||||59|-1||SNV|HGNC|7106|,T|downstream_gene_variant|MODIFIER|ATXN3|ENSG00000066427|Transcript|ENST00000554350|nonsense_mediated_decay|||||-/943|-/333|-/110||||59|-1||SNV|HGNC|7106| ATXN3 ENSG00000066427 ENST00000532032 0.0494 0.90185 0.04875 Tolerant 15 89436295 . G A 449.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.041;ClippingRankSum=-0.954;DP=30;FS=1.455;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.290;POSITIVE_TRAIN_SITE;QD=14.99;ReadPosRankSum=-1.120;VQSLOD=4.35;culprit=FS;CSQ=A|intron_variant|MODIFIER|HAPLN3|ENSG00000140511|Transcript|ENST00000562281|protein_coding||1/4|||-/801|-/679|-/226|||||-1||SNV|HGNC|21446|,A|intron_variant&NMD_transcript_variant|MODIFIER|HAPLN3|ENSG00000140511|Transcript|ENST00000558770|nonsense_mediated_decay||1/5|||-/3071|-/561|-/186|||||-1||SNV|HGNC|21446|,A|intron_variant&non_coding_transcript_variant|MODIFIER|HAPLN3|ENSG00000140511|Transcript|ENST00000563808|retained_intron||1/2|||-/807|||||||-1||SNV|HGNC|21446|,A|intron_variant|MODIFIER|HAPLN3|ENSG00000140511|Transcript|ENST00000359595|protein_coding||1/4|||-/1980|-/1083|-/360|||||-1|1|SNV|HGNC|21446|NM_178232.2,A|stop_gained|HIGH|HAPLN3|ENSG00000140511|Transcript|ENST00000562889|protein_coding|2/6||||188/1547|49/1269|17/422|Q/*|Cag/Tag|||-1||SNV|HGNC|21446| HAPLN3 ENSG00000140511 ENST00000562889 0.0223 0.8723 0.1054 Tolerant 15 97327393 . C T 653.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.961;ClippingRankSum=-0.021;DP=32;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.227;POSITIVE_TRAIN_SITE;QD=20.43;ReadPosRankSum=-0.268;VQSLOD=5.32;culprit=FS;CSQ=T|stop_gained|HIGH|SPATA8|ENSG00000185594|Transcript|ENST00000328504|protein_coding|2/3||||367/1083|100/318|34/105|R/*|Cga/Tga|||1|1|SNV|HGNC|28676|NM_173499.3,T|5_prime_UTR_variant|MODIFIER|SPATA8|ENSG00000185594|Transcript|ENST00000558553|protein_coding|2/3||||127/406|-/207|-/68|||||1||SNV|HGNC|28676|,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|SPATA8|ENSG00000185594|Transcript|ENST00000561002|retained_intron|2/3||||393/569|||||||1||SNV|HGNC|28676|,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|SPATA8|ENSG00000185594|Transcript|ENST00000560327|retained_intron|1/2||||677/1386|||||||1||SNV|HGNC|28676|,T|upstream_gene_variant|MODIFIER|SPATA8-AS1|ENSG00000259282|Transcript|ENST00000560888|antisense|||||-/392||||||2509|-1||SNV|HGNC|48627|,T|upstream_gene_variant|MODIFIER|SPATA8-AS1|ENSG00000259282|Transcript|ENST00000558722|antisense|||||-/465||||||851|-1||SNV|HGNC|48627| SPATA8 ENSG00000185594 ENST00000328504 0.00175 0.9845 0.01375 Tolerant 16 81242198 . G A 462.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.045;ClippingRankSum=0.896;DP=28;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.861;POSITIVE_TRAIN_SITE;QD=16.53;ReadPosRankSum=-1.815;VQSLOD=3.97;culprit=FS;CSQ=A|stop_gained|HIGH|PKD1L2|ENSG00000166473|Transcript|ENST00000525539|polymorphic_pseudogene|4/43||||658/7379|658/7379|220/2459|Q/*|Cag/Tag|||-1||SNV|HGNC|21715|NM_052892.3,A|stop_gained|HIGH|PKD1L2|ENSG00000166473|Transcript|ENST00000337114|protein_coding|4/18||||658/3427|658/2976|220/991|Q/*|Cag/Tag|||-1|1|SNV|HGNC|21715|NM_001076780.1 PKD1L2 ENSG00000166473 ENST00000525539 0.0018 0.98645 0.01175 Tolerant 17 14005439 . G A 635.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.521;ClippingRankSum=-2.282;DP=36;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.982;POSITIVE_TRAIN_SITE;QD=17.66;ReadPosRankSum=1.014;VQSLOD=5.38;culprit=FS;CSQ=A|synonymous_variant|LOW|COX10|ENSG00000006695|Transcript|ENST00000261643|protein_coding|4/7||||581/2873|504/1332|168/443|L|ctG/ctA|||1|1|SNV|HGNC|2260|NM_001303.3,A|stop_gained&NMD_transcript_variant|HIGH|COX10|ENSG00000006695|Transcript|ENST00000580561|nonsense_mediated_decay|3/6||||184/1384|182/189|61/62|W/*|tGg/tAg|||1||SNV|HGNC|2260|,A|5_prime_UTR_variant|MODIFIER|COX10|ENSG00000006695|Transcript|ENST00000537334|protein_coding|3/6||||184/1384|-/681|-/226|||||1||SNV|HGNC|2260|,A|intron_variant&NMD_transcript_variant|MODIFIER|COX10|ENSG00000006695|Transcript|ENST00000581931|nonsense_mediated_decay||3/5|||-/1509|-/507|-/168|||||1||SNV|HGNC|2260|,A|intron_variant|MODIFIER|COX10|ENSG00000006695|Transcript|ENST00000536205|protein_coding||3/5|||-/1509|-/756|-/251|||||1||SNV|HGNC|2260| COX10 ENSG00000006695 ENST00000580561 0.01575 0.81975 0.1645 Tolerant 17 33772658 . G T 958.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.735;ClippingRankSum=-0.432;DP=60;FS=5.208;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.280;POSITIVE_TRAIN_SITE;QD=15.98;ReadPosRankSum=0.356;VQSLOD=3.44;culprit=FS;CSQ=T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000526861|protein_coding|4/7||||300/6004|42/2694|14/897|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|stop_gained&NMD_transcript_variant|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000530782|nonsense_mediated_decay|3/7||||318/3910|42/360|14/119|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000285013|protein_coding|3/6||||318/8469|42/2694|14/897|Y/*|taC/taA|||-1|1|SNV|HGNC|26481|NM_144682.5,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000531588|protein_coding|4/4||||359/550|42/233|14/77|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|downstream_gene_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000526483|retained_intron|||||-/463||||||1347|-1||SNV|HGNC|26481|,T|upstream_gene_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000532774|retained_intron|||||-/563||||||1685|-1||SNV|HGNC|26481|,T|intron_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000532210|protein_coding||2/4|||-/596|-/392|-/130|||||-1||SNV|HGNC|26481|,T|intron_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000360502|protein_coding||1/4|||-/7239|-/1740|-/579|||||-1||SNV|HGNC|26481|,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000524511|protein_coding|3/3||||299/576|42/319|14/106|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000542635|protein_coding|3/6||||219/5921|42/2694|14/897|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|intron_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000534689|protein_coding||3/6|||-/3058|-/1740|-/579|||||-1||SNV|HGNC|26481|,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000533791|protein_coding|1/4||||372/4121|42/2694|14/897|Y/*|taC/taA|||-1||SNV|HGNC|26481| SLFN13 ENSG00000154760 ENST00000530782 0.00435 0.90635 0.0893 Tolerant 17 33772658 . G T 958.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.735;ClippingRankSum=-0.432;DP=60;FS=5.208;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.280;POSITIVE_TRAIN_SITE;QD=15.98;ReadPosRankSum=0.356;VQSLOD=3.44;culprit=FS;CSQ=T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000526861|protein_coding|4/7||||300/6004|42/2694|14/897|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|stop_gained&NMD_transcript_variant|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000530782|nonsense_mediated_decay|3/7||||318/3910|42/360|14/119|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000285013|protein_coding|3/6||||318/8469|42/2694|14/897|Y/*|taC/taA|||-1|1|SNV|HGNC|26481|NM_144682.5,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000531588|protein_coding|4/4||||359/550|42/233|14/77|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|downstream_gene_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000526483|retained_intron|||||-/463||||||1347|-1||SNV|HGNC|26481|,T|upstream_gene_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000532774|retained_intron|||||-/563||||||1685|-1||SNV|HGNC|26481|,T|intron_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000532210|protein_coding||2/4|||-/596|-/392|-/130|||||-1||SNV|HGNC|26481|,T|intron_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000360502|protein_coding||1/4|||-/7239|-/1740|-/579|||||-1||SNV|HGNC|26481|,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000524511|protein_coding|3/3||||299/576|42/319|14/106|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000542635|protein_coding|3/6||||219/5921|42/2694|14/897|Y/*|taC/taA|||-1||SNV|HGNC|26481|,T|intron_variant|MODIFIER|SLFN13|ENSG00000154760|Transcript|ENST00000534689|protein_coding||3/6|||-/3058|-/1740|-/579|||||-1||SNV|HGNC|26481|,T|stop_gained|HIGH|SLFN13|ENSG00000154760|Transcript|ENST00000533791|protein_coding|1/4||||372/4121|42/2694|14/897|Y/*|taC/taA|||-1||SNV|HGNC|26481| SLFN13 ENSG00000154760 ENST00000285013 0.0029 0.9743 0.0228 Tolerant 17 36894839 . G A 518.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=1.951;ClippingRankSum=-1.206;DP=29;FS=1.462;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.425;POSITIVE_TRAIN_SITE;QD=17.89;ReadPosRankSum=1.031;VQSLOD=2.79;culprit=FS;CSQ=A|stop_gained|HIGH|PCGF2|ENSG00000056661|Transcript|ENST00000578109|protein_coding|6/9||||485/1196|277/612|93/203|R/*|Cga/Tga|||-1||SNV|HGNC|12929|,A|downstream_gene_variant|MODIFIER|CISD3|ENSG00000230055|Transcript|ENST00000578573|processed_transcript|||||-/2326||||||3542|1||SNV|HGNC|27578|,A|stop_gained|HIGH|PCGF2|ENSG00000056661|Transcript|ENST00000579882|protein_coding|8/11||||755/1534|439/774|147/257|R/*|Cga/Tga|||-1||SNV|HGNC|12929|,A|stop_gained|HIGH|PCGF2|ENSG00000056661|Transcript|ENST00000585100|protein_coding|7/10||||785/1499|439/774|147/257|R/*|Cga/Tga|||-1||SNV|HGNC|12929|,A|downstream_gene_variant|MODIFIER|CISD3|ENSG00000230055|Transcript|ENST00000439660|protein_coding|||||-/2074|-/384|-/127||||3565|1||SNV|HGNC|27578|NM_001136498.1,A|downstream_gene_variant|MODIFIER|CISD3|ENSG00000230055|Transcript|ENST00000581668|retained_intron|||||-/773||||||4871|1||SNV|HGNC|27578|,A|upstream_gene_variant|MODIFIER|PCGF2|ENSG00000056661|Transcript|ENST00000578487|protein_coding|||||-/459|-/201|-/66||||2990|-1||SNV|HGNC|12929|,A|synonymous_variant|LOW|PCGF2|ENSG00000056661|Transcript|ENST00000581345|protein_coding|7/10||||636/2179|435/1035|145/344|D|gaC/gaT|||-1||SNV|HGNC|12929|,A|synonymous_variant|LOW|PCGF2|ENSG00000056661|Transcript|ENST00000360797|protein_coding|8/11||||678/2604|435/1035|145/344|D|gaC/gaT|||-1||SNV|HGNC|12929|NM_007144.2,A|synonymous_variant|LOW|PCGF2|ENSG00000056661|Transcript|ENST00000580830|protein_coding|9/12||||1137/3062|435/1035|145/344|D|gaC/gaT|||-1|1|SNV|HGNC|12929| PCGF2 ENSG00000056661 ENST00000579882 0.0235 0.8979 0.0786 Tolerant 17 45425287 . C T 565.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.780;ClippingRankSum=-1.542;DP=46;FS=2.588;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.024;POSITIVE_TRAIN_SITE;QD=12.30;ReadPosRankSum=0.191;VQSLOD=3.50;culprit=FS;CSQ=T|intron_variant|MODIFIER|EFCAB13|ENSG00000178852|Transcript|ENST00000517310|protein_coding||9/10|||-/1477|-/313|-/104|||||1||SNV|HGNC|26864|,T|downstream_gene_variant|MODIFIER|ITGB3|ENSG00000259207|Transcript|ENST00000435993|protein_coding|||||-/2785|-/2256|-/751||||3629|1||SNV|HGNC|6156|,T|downstream_gene_variant|MODIFIER|ITGB3|ENSG00000259753|Transcript|ENST00000560629|nonsense_mediated_decay|||||-/2785|-/2364|-/787||||3629|1||SNV|Uniprot_gn|6156|,T|intron_variant|MODIFIER|EFCAB13|ENSG00000178852|Transcript|ENST00000517484|protein_coding||8/21|||-/3466|-/2355|-/784|||||1||SNV|HGNC|26864|NM_001195192.1,T|intron_variant&non_coding_transcript_variant|MODIFIER|EFCAB13|ENSG00000178852|Transcript|ENST00000520776|retained_intron||6/13|||-/1979|||||||1||SNV|HGNC|26864|,T|stop_gained|HIGH|EFCAB13|ENSG00000178852|Transcript|ENST00000331493|protein_coding|9/25||||1042/3931|631/2922|211/973|R/*|Cga/Tga|||1|1|SNV|HGNC|26864|NM_152347.4 EFCAB13 ENSG00000178852 ENST00000331493 0.00455 0.95965 0.0358 Tolerant 17 61829719 . A C 699.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.598;ClippingRankSum=1.364;DP=39;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.812;QD=17.94;ReadPosRankSum=-0.996;VQSLOD=3.57;culprit=FS;CSQ=C|downstream_gene_variant|MODIFIER|CCDC47|ENSG00000108588|Transcript|ENST00000582331|retained_intron|||||-/693||||||421|-1||SNV|HGNC|24856|,C|stop_gained|HIGH|CCDC47|ENSG00000108588|Transcript|ENST00000582252|protein_coding|11/12||||1342/1719|1164/1443|388/480|Y/*|taT/taG|||-1||SNV|HGNC|24856|,C|stop_gained|HIGH|CCDC47|ENSG00000108588|Transcript|ENST00000225726|protein_coding|11/13||||1547/3466|1164/1452|388/483|Y/*|taT/taG|||-1|1|SNV|HGNC|24856|NM_020198.2,C|stop_gained|HIGH|CCDC47|ENSG00000108588|Transcript|ENST00000403162|protein_coding|12/14||||1429/2195|1164/1452|388/483|Y/*|taT/taG|||-1||SNV|HGNC|24856|,C|upstream_gene_variant|MODIFIER|RP11-51F16.8|ENSG00000125695|Transcript|ENST00000580553|nonsense_mediated_decay|||||-/2128|-/165|-/54||||262|-1||SNV|Clone_based_vega_gene|| CCDC47 ENSG00000108588 ENST00000225726 0.31735 0.0746 0.60805 Recessive 18 25616451 . A T 898.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.588;ClippingRankSum=-1.263;DP=56;FS=1.067;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.003;POSITIVE_TRAIN_SITE;QD=16.05;ReadPosRankSum=-0.294;VQSLOD=3.92;culprit=FS;CSQ=T|intron_variant|MODIFIER|CDH2|ENSG00000170558|Transcript|ENST00000413878|protein_coding||2/3|||-/563|-/219|-/73|||||-1||SNV|HGNC|1759|,T|intron_variant|MODIFIER|CDH2|ENSG00000170558|Transcript|ENST00000418492|protein_coding||1/4|||-/740|-/573|-/191|||||-1||SNV|HGNC|1759|,T|stop_gained|HIGH|CDH2|ENSG00000170558|Transcript|ENST00000399380|protein_coding|1/15||||99/3737|62/2628|21/875|L/*|tTg/tAg|||-1||SNV|HGNC|1759|,T|intron_variant|MODIFIER|CDH2|ENSG00000170558|Transcript|ENST00000269141|protein_coding||2/15|||-/4332|-/2721|-/906|||||-1|1|SNV|HGNC|1759|NM_001792.3,T|intron_variant|MODIFIER|CDH2|ENSG00000170558|Transcript|ENST00000430882|protein_coding||1/3|||-/610|-/360|-/120|||||-1||SNV|HGNC|1759| CDH2 ENSG00000170558 ENST00000399380 0.03265 0.88115 0.0862 Tolerant 19 759925 . C A 541.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.652;ClippingRankSum=-0.310;DP=34;FS=1.356;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.827;QD=15.93;ReadPosRankSum=-0.896;VQSLOD=2.83;culprit=FS;CSQ=A|stop_gained|HIGH|MISP|ENSG00000099812|Transcript|ENST00000215582|protein_coding|3/5||||1900/2872|1797/2040|599/679|Y/*|taC/taA|||1|1|SNV|HGNC|27000|NM_173481.2 MISP ENSG00000099812 ENST00000215582 0.09755 0.26395 0.6385 Recessive 19 4659924 . C T 556.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.196;ClippingRankSum=-1.187;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.743;POSITIVE_TRAIN_SITE;QD=13.58;ReadPosRankSum=1.135;VQSLOD=4.51;culprit=FS;CSQ=T|intron_variant|MODIFIER|C19orf10|ENSG00000074842|Transcript|ENST00000262947|protein_coding||5/5|||-/1018|-/522|-/173|||||-1|1|SNV|HGNC|16948|NM_019107.3,T|intron_variant|MODIFIER|C19orf10|ENSG00000074842|Transcript|ENST00000599761|protein_coding||3/3|||-/463|-/255|-/84|||||-1||SNV|HGNC|16948|,T|downstream_gene_variant|MODIFIER|TNFAIP8L1|ENSG00000185361|Transcript|ENST00000536716|protein_coding|||||-/3845|-/561|-/186||||4344|1||SNV|HGNC|28279|NM_001167942.1,T|stop_gained|HIGH|C19orf10|ENSG00000074842|Transcript|ENST00000599630|protein_coding|5/5||||489/713|461/570|154/189|W/*|tGg/tAg|||-1||SNV|HGNC|16948|,T|upstream_gene_variant|MODIFIER|AC005339.2|ENSG00000268565|Transcript|ENST00000598070|antisense|||||-/392||||||4388|-1||SNV|Clone_based_vega_gene||,T|downstream_gene_variant|MODIFIER|C19orf10|ENSG00000074842|Transcript|ENST00000596031|retained_intron|||||-/335||||||668|-1||SNV|HGNC|16948|,T|downstream_gene_variant|MODIFIER|TNFAIP8L1|ENSG00000185361|Transcript|ENST00000327473|protein_coding|||||-/3814|-/561|-/186||||4344|1||SNV|HGNC|28279|NM_152362.2 C19orf10 ENSG00000074842 ENST00000599630 0.0028 0.9634 0.0338 Tolerant 19 35719020 . C T 396.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=2.647;ClippingRankSum=-0.499;DP=32;FS=5.514;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.765;POSITIVE_TRAIN_SITE;QD=12.40;ReadPosRankSum=0.537;VQSLOD=3.09;culprit=MQRankSum;CSQ=T|downstream_gene_variant|MODIFIER|FAM187B2P|ENSG00000262497|Transcript|ENST00000577135|unprocessed_pseudogene|||||-/713||||||4174|-1||SNV|HGNC|49213|,T|stop_gained|HIGH|FAM187B|ENSG00000177558|Transcript|ENST00000324675|protein_coding|1/2||||613/1184|564/1110|188/369|W/*|tgG/tgA|||-1|1|SNV|HGNC|26366|NM_152481.1 FAM187B ENSG00000177558 ENST00000324675 0.00035 0.99085 0.0088 Tolerant 19 49206674 . G A 1129.77 PASS AC=2;AF=1.00;AN=2;DP=34;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=33.23;VQSLOD=5.95;culprit=FS;CSQ=A|stop_gained|HIGH|FUT2|ENSG00000176920|Transcript|ENST00000425340|protein_coding|2/2||||578/3111|461/1032|154/343|W/*|tGg/tAg|||1|1|SNV|HGNC|4013|NM_001097638.2&NM_000511.5,A|stop_gained|HIGH|FUT2|ENSG00000176920|Transcript|ENST00000391876|protein_coding|2/3||||568/1468|461/1032|154/343|W/*|tGg/tAg|||1||SNV|HGNC|4013|,A|stop_gained|HIGH|FUT2|ENSG00000176920|Transcript|ENST00000522966|protein_coding|2/2||||572/771|461/660|154/220|W/*|tGg/tAg|||1||SNV|HGNC|4013| FUT2 ENSG00000176920 ENST00000425340 0.0058 0.87195 0.12225 Tolerant 19 52004903 . G A 437.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.246;ClippingRankSum=-0.982;DP=32;FS=1.340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.586;POSITIVE_TRAIN_SITE;QD=13.68;ReadPosRankSum=-0.415;VQSLOD=4.48;culprit=FS;CSQ=A|stop_gained|HIGH|SIGLEC12|ENSG00000254521|Transcript|ENST00000291707|protein_coding|1/8||||141/2121|85/1788|29/595|Q/*|Cag/Tag|||-1|1|SNV|HGNC|15482|NM_053003.2,A|upstream_gene_variant|MODIFIER|SIGLEC12|ENSG00000254521|Transcript|ENST00000598614|protein_coding|||||-/1434|-/1434|-/477||||1276|-1||SNV|HGNC|15482|NM_033329.1,A|stop_gained&NMD_transcript_variant|HIGH|SIGLEC12|ENSG00000254521|Transcript|ENST00000596742|nonsense_mediated_decay|1/8||||124/1791|85/465|29/154|Q/*|Cag/Tag|||-1||SNV|HGNC|15482|,A|downstream_gene_variant|MODIFIER|CTD-3073N11.7|ENSG00000268839|Transcript|ENST00000594712|unprocessed_pseudogene|||||-/304||||||3410|-1||SNV|Clone_based_vega_gene|| SIGLEC12 ENSG00000254521 ENST00000291707 0.00095 0.98985 0.0092 Tolerant 19 52004903 . G A 437.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.246;ClippingRankSum=-0.982;DP=32;FS=1.340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.586;POSITIVE_TRAIN_SITE;QD=13.68;ReadPosRankSum=-0.415;VQSLOD=4.48;culprit=FS;CSQ=A|stop_gained|HIGH|SIGLEC12|ENSG00000254521|Transcript|ENST00000291707|protein_coding|1/8||||141/2121|85/1788|29/595|Q/*|Cag/Tag|||-1|1|SNV|HGNC|15482|NM_053003.2,A|upstream_gene_variant|MODIFIER|SIGLEC12|ENSG00000254521|Transcript|ENST00000598614|protein_coding|||||-/1434|-/1434|-/477||||1276|-1||SNV|HGNC|15482|NM_033329.1,A|stop_gained&NMD_transcript_variant|HIGH|SIGLEC12|ENSG00000254521|Transcript|ENST00000596742|nonsense_mediated_decay|1/8||||124/1791|85/465|29/154|Q/*|Cag/Tag|||-1||SNV|HGNC|15482|,A|downstream_gene_variant|MODIFIER|CTD-3073N11.7|ENSG00000268839|Transcript|ENST00000594712|unprocessed_pseudogene|||||-/304||||||3410|-1||SNV|Clone_based_vega_gene|| SIGLEC12 ENSG00000254521 ENST00000596742 0.00635 0.90075 0.0929 Tolerant 19 52096053 . T A 617.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.948;ClippingRankSum=0.352;DP=40;FS=1.278;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.327;POSITIVE_TRAIN_SITE;QD=15.44;ReadPosRankSum=-0.379;VQSLOD=4.52;culprit=MQRankSum;CSQ=A|stop_gained|HIGH|AC018755.1|ENSG00000167765|Transcript|ENST00000301439|protein_coding|2/2||||681/1698|625/789|209/262|K/*|Aaa/Taa|||-1|1|SNV|Clone_based_ensembl_gene||,A|downstream_gene_variant|MODIFIER|ZNF175|ENSG00000105497|Transcript|ENST00000436511|protein_coding|||||-/488|-/339|-/112||||3062|1||SNV|HGNC|12964|,A|downstream_gene_variant|MODIFIER|ZNF175|ENSG00000105497|Transcript|ENST00000262259|protein_coding|||||-/3742|-/2136|-/711||||3085|1||SNV|HGNC|12964|NM_007147.2,A|upstream_gene_variant|MODIFIER|AC018755.16|ENSG00000269388|Transcript|ENST00000598755|processed_transcript|||||-/664||||||1761|1||SNV|Clone_based_vega_gene|| AC018755.1 ENSG00000167765 ENST00000301439 0.0014 0.97905 0.01955 Tolerant 19 57642782 . C A 1752.77 PASS AC=2;AF=1.00;AN=2;DP=45;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.04;VQSLOD=5.79;culprit=FS;CSQ=A|downstream_gene_variant|MODIFIER|USP29|ENSG00000131864|Transcript|ENST00000600940|protein_coding|||||-/533|-/39|-/13||||2700|1||SNV|HGNC|18563|,A|stop_gained|HIGH|USP29|ENSG00000131864|Transcript|ENST00000598197|protein_coding|1/1||||2772/3284|2739/2769|913/922|Y/*|taC/taA|||1||SNV|HGNC|18563|,A|downstream_gene_variant|MODIFIER|ZIM3|ENSG00000141946|Transcript|ENST00000269834|protein_coding|||||-/2627|-/1419|-/472||||2682|-1||SNV|HGNC|16366|NM_052882.1,A|downstream_gene_variant|MODIFIER|U3|ENSG00000252683|Transcript|ENST00000516874|snoRNA|||||-/218||||||2636|-1||SNV|RFAM||,A|stop_gained|HIGH|USP29|ENSG00000131864|Transcript|ENST00000254181|protein_coding|4/4||||3193/3705|2739/2769|913/922|Y/*|taC/taA|||1|1|SNV|HGNC|18563|NM_020903.2,A|downstream_gene_variant|MODIFIER|USP29|ENSG00000131864|Transcript|ENST00000600020|protein_coding|||||-/437|-/92|-/30||||2647|1||SNV|HGNC|18563| USP29 ENSG00000131864 ENST00000254181 0.0058 0.9612 0.033 Tolerant 19 57646393 . T A 804.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-0.776;ClippingRankSum=-1.785;DP=52;FS=8.059;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.194;POSITIVE_TRAIN_SITE;QD=15.48;ReadPosRankSum=1.669;VQSLOD=2.60;culprit=FS;CSQ=A|downstream_gene_variant|MODIFIER|USP29|ENSG00000131864|Transcript|ENST00000598197|protein_coding|||||-/3284|-/2769|-/922||||3099|1||SNV|HGNC|18563|,A|stop_gained|HIGH|ZIM3|ENSG00000141946|Transcript|ENST00000269834|protein_coding|5/5||||1698/2627|1312/1419|438/472|K/*|Aaa/Taa|||-1|1|SNV|HGNC|16366|NM_052882.1,A|upstream_gene_variant|MODIFIER|U3|ENSG00000252683|Transcript|ENST00000516874|snoRNA|||||-/218||||||758|-1||SNV|RFAM||,A|downstream_gene_variant|MODIFIER|USP29|ENSG00000131864|Transcript|ENST00000254181|protein_coding|||||-/3705|-/2769|-/922||||3099|1||SNV|HGNC|18563|NM_020903.2 ZIM3 ENSG00000141946 ENST00000269834 0.00445 0.9653 0.03025 Tolerant 20 20033242 . A T 471.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=-1.674;ClippingRankSum=-0.251;DP=31;FS=1.497;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.502;POSITIVE_TRAIN_SITE;QD=15.22;ReadPosRankSum=1.172;VQSLOD=4.10;culprit=FS;CSQ=T|upstream_gene_variant|MODIFIER|C20orf26|ENSG00000089101|Transcript|ENST00000451767|protein_coding|||||-/1946|-/1413|-/470||||4048|1||SNV|HGNC|15872|NM_001167816.1,T|5_prime_UTR_variant|MODIFIER|C20orf26|ENSG00000089101|Transcript|ENST00000475466|protein_coding|1/5||||20/569|-/407|-/135|||||1||SNV|HGNC|15872|,T|synonymous_variant|LOW|CRNKL1|ENSG00000101343|Transcript|ENST00000377327|protein_coding|2/15||||224/4370|192/2511|64/836|V|gtT/gtA|||-1||SNV|HGNC|15762|NM_001278626.1&NM_001278625.1&NM_001278627.1,T|splice_region_variant&intron_variant|LOW|C20orf26|ENSG00000089101|Transcript|ENST00000377306|protein_coding||1/13|||-/2017|-/1413|-/470|||||1||SNV|HGNC|15872|,T|splice_region_variant&intron_variant|LOW|C20orf26|ENSG00000089101|Transcript|ENST00000245957|protein_coding||1/26|||-/4082|-/3714|-/1237|||||1|1|SNV|HGNC|15872|NM_015585.3,T|synonymous_variant&NMD_transcript_variant|LOW|CRNKL1|ENSG00000101343|Transcript|ENST00000490910|nonsense_mediated_decay|2/15||||224/4183|192/315|64/104|V|gtT/gtA|||-1||SNV|HGNC|15762|,T|splice_region_variant&intron_variant|LOW|C20orf26|ENSG00000089101|Transcript|ENST00000389656|protein_coding||1/21|||-/2649|-/603|-/200|||||1||SNV|HGNC|15872|,T|splice_region_variant&intron_variant|LOW|C20orf26|ENSG00000089101|Transcript|ENST00000377309|protein_coding||1/25|||-/3792|-/963|-/320|||||1||SNV|HGNC|15872|,T|synonymous_variant|LOW|CRNKL1|ENSG00000101343|Transcript|ENST00000377340|protein_coding|2/15||||260/4406|228/2547|76/848|V|gtT/gtA|||-1||SNV|HGNC|15762|NM_016652.5,T|splice_region_variant&intron_variant&NMD_transcript_variant|LOW|C20orf26|ENSG00000089101|Transcript|ENST00000494029|nonsense_mediated_decay||1/4|||-/570|-/168|-/55|||||1||SNV|HGNC|15872|,T|5_prime_UTR_variant|MODIFIER|C20orf26|ENSG00000089101|Transcript|ENST00000377303|protein_coding|1/6||||41/679|-/567|-/189|||||1||SNV|HGNC|15872|,T|splice_region_variant&intron_variant|LOW|C20orf26|ENSG00000089101|Transcript|ENST00000340348|protein_coding||1/10|||-/1185|-/1112|-/370|||||1||SNV|HGNC|15872|,T|stop_gained&NMD_transcript_variant|HIGH|CRNKL1|ENSG00000101343|Transcript|ENST00000496549|nonsense_mediated_decay|2/15||||130/4093|98/225|33/74|L/*|tTa/tAa|||-1||SNV|HGNC|15762|,T|upstream_gene_variant|MODIFIER|CRNKL1|ENSG00000101343|Transcript|ENST00000536226|protein_coding|||||-/4009|-/2064|-/687||||132|-1||SNV|HGNC|15762|NM_001278628.1 CRNKL1 ENSG00000101343 ENST00000496549 0.00575 0.9651 0.02915 Tolerant 21 31744127 . A T 1199.77 PASS AC=2;AF=1.00;AN=2;DP=33;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=28.76;VQSLOD=5.81;culprit=FS;CSQ=T|stop_gained|HIGH|KRTAP13-2|ENSG00000182816|Transcript|ENST00000399889|protein_coding|1/1||||431/849|405/528|135/175|C/*|tgT/tgA|||-1|1|SNV|HGNC|18923|NM_181621.3,T|downstream_gene_variant|MODIFIER|MIR4327|ENSG00000265007|Transcript|ENST00000581194|miRNA|||||-/85||||||3485|-1||SNV|HGNC|38355| KRTAP13-2 ENSG00000182816 ENST00000399889 0.0016 0.9852 0.0132 Tolerant 22 17469049 . C A 600.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.398;ClippingRankSum=-0.875;DP=37;FS=1.301;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.366;POSITIVE_TRAIN_SITE;QD=16.24;ReadPosRankSum=0.111;VQSLOD=4.21;culprit=FS;CSQ=A|intron_variant&NMD_transcript_variant|MODIFIER|GAB4|ENSG00000215568|Transcript|ENST00000465611|nonsense_mediated_decay||2/8|||-/2698|-/576|-/191|||||-1||SNV|HGNC|18325|,A|stop_gained|HIGH|GAB4|ENSG00000215568|Transcript|ENST00000400588|protein_coding|3/10||||595/2630|487/1725|163/574|G/*|Gga/Tga|||-1|1|SNV|HGNC|18325|NM_001037814.1,A|intron_variant&non_coding_transcript_variant|MODIFIER|GAB4|ENSG00000215568|Transcript|ENST00000523144|processed_transcript||2/3|||-/594|||||||-1||SNV|HGNC|18325| GAB4 ENSG00000215568 ENST00000400588 0.0035 0.96955 0.02695 Tolerant 22 50705304 . C T 362.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.992;ClippingRankSum=0.461;DP=35;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.461;POSITIVE_TRAIN_SITE;QD=10.36;ReadPosRankSum=-0.425;VQSLOD=5.24;culprit=FS;CSQ=T|intron_variant&NMD_transcript_variant|MODIFIER|MAPK11|ENSG00000185386|Transcript|ENST00000417877|nonsense_mediated_decay||7/11|||-/2409|-/492|-/163|||||-1||SNV|HGNC|6873|,T|downstream_gene_variant|MODIFIER|MAPK11|ENSG00000185386|Transcript|ENST00000495277|processed_transcript|||||-/566||||||263|-1||SNV|HGNC|6873|,T|intron_variant|MODIFIER|MAPK11|ENSG00000185386|Transcript|ENST00000330651|protein_coding||7/11|||-/2431|-/1095|-/364|||||-1|1|SNV|HGNC|6873|NM_002751.5,T|stop_gained|HIGH|MAPK11|ENSG00000185386|Transcript|ENST00000449719|protein_coding|6/6||||682/1408|345/642|115/213|W/*|tgG/tgA|||-1||SNV|HGNC|6873|,T|intron_variant&NMD_transcript_variant|MODIFIER|MAPK11|ENSG00000185386|Transcript|ENST00000395764|nonsense_mediated_decay||7/12|||-/1512|-/1095|-/364|||||-1||SNV|HGNC|6873| MAPK11 ENSG00000185386 ENST00000449719 0.03545 0.89115 0.0734 Tolerant X 35821127 . C T 1109.77 PASS AC=2;AF=1.00;AN=2;DP=28;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;POSITIVE_TRAIN_SITE;QD=29.57;VQSLOD=5.86;culprit=FS;CSQ=T|stop_gained|HIGH|MAGEB16|ENSG00000189023|Transcript|ENST00000399987|protein_coding|3/3||||1011/1736|814/975|272/324|R/*|Cga/Tga|||1||SNV|HGNC|21188|,T|stop_gained|HIGH|MAGEB16|ENSG00000189023|Transcript|ENST00000399992|protein_coding|3/3||||1009/1734|910/1071|304/356|R/*|Cga/Tga|||1||SNV|HGNC|21188|,T|stop_gained|HIGH|MAGEB16|ENSG00000189023|Transcript|ENST00000399988|protein_coding|2/2||||957/1682|814/975|272/324|R/*|Cga/Tga|||1||SNV|HGNC|21188|,T|stop_gained|HIGH|MAGEB16|ENSG00000189023|Transcript|ENST00000399985|protein_coding|2/2||||942/1667|814/975|272/324|R/*|Cga/Tga|||1||SNV|HGNC|21188|,T|stop_gained|HIGH|MAGEB16|ENSG00000189023|Transcript|ENST00000399989|protein_coding|2/2||||1093/1818|814/975|272/324|R/*|Cga/Tga|||1|1|SNV|HGNC|21188|NM_001099921.1 MAGEB16 ENSG00000189023 ENST00000399989 0.00365 0.9318 0.06455 Tolerant X 142967468 . T G 795.77 PASS AC=2;AF=1.00;AN=2;BaseQRankSum=1.583;ClippingRankSum=0.226;DP=23;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;MQRankSum=-0.528;POSITIVE_TRAIN_SITE;QD=34.60;ReadPosRankSum=-1.583;VQSLOD=1.38;culprit=FS;CSQ=G|stop_gained|HIGH|UBE2NL|ENSG00000102069|Transcript|ENST00000370494|protein_coding|1/1||||296/1183|266/462|89/153|L/*|tTa/tGa|||1|1|SNV|HGNC|31710|NM_001012989.1 UBE2NL ENSG00000102069 ENST00000370494 0.01375 0.9226 0.06365 Tolerant