1	979496	.	T	C	.	.	CSQ=C|missense_variant|MODERATE|PERM1|ENSG00000187642|Transcript|ENST00000341290|protein_coding|3/5||ENST00000341290.6:c.1192A>G|ENSP00000343864.2:p.Ser398Gly|1228|1192|398|S/G|Agc/Ggc|rs13302983||-1||SNV|HGNC|HGNC:28208|||2|A2||ENSP00000343864|Q5SV97||||tolerated(0.2)|benign(0.003)|PANTHER:PTHR47282&MobiDB_lite:mobidb-lite||||0.9418|0.9539|0.999|0.9592|0.9847|||0.9721|0.9533|0.9754|0.9166|0.9999|0.9923|0.9677|0.9536|0.9811|0.9999|gnomAD_EAS|||||||||||||||||||-27|-2|23|25|0.00|0.00|0.00|0.00|PERM1,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407|protein_coding||||||||||rs13302983|4488|1||SNV|HGNC|HGNC:25284|||1|A2|CCDS53256.1|ENSP00000368717|Q494U1||||||||||0.9418|0.9539|0.999|0.9592|0.9847|||0.9721|0.9533|0.9754|0.9166|0.9999|0.9923|0.9677|0.9536|0.9811|0.9999|gnomAD_EAS|||||||||||||||||||-27|-2|23|25|0.00|0.00|0.00|0.00|PERM1,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409|protein_coding||||||||||rs13302983|4488|1||SNV|HGNC|HGNC:25284|||2|A2||ENSP00000368719|Q494U1||||||||||0.9418|0.9539|0.999|0.9592|0.9847|||0.9721|0.9533|0.9754|0.9166|0.9999|0.9923|0.9677|0.9536|0.9811|0.9999|gnomAD_EAS|||||||||||||||||||-27|-2|23|25|0.00|0.00|0.00|0.00|PERM1,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410|protein_coding||||||||||rs13302983|3631|1||SNV|HGNC|HGNC:25284|YES|NM_032129.3|1|P3|CCDS4.1|ENSP00000368720|Q494U1||UPI00001416D8||||||||0.9418|0.9539|0.999|0.9592|0.9847|||0.9721|0.9533|0.9754|0.9166|0.9999|0.9923|0.9677|0.9536|0.9811|0.9999|gnomAD_EAS|||||||||||||||||||-27|-2|23|25|0.00|0.00|0.00|0.00|PERM1,C|missense_variant|MODERATE|PERM1|ENSG00000187642|Transcript|ENST00000433179|protein_coding|1/3||ENST00000433179.3:c.1534A>G|ENSP00000414022.3:p.Ser512Gly|1534|1534|512|S/G|Agc/Ggc|rs13302983||-1||SNV|HGNC|HGNC:28208|YES||5|P2|CCDS76083.1|ENSP00000414022|Q5SV97||||tolerated(0.18)|benign(0.011)|PANTHER:PTHR47282&MobiDB_lite:mobidb-lite||||0.9418|0.9539|0.999|0.9592|0.9847|||0.9721|0.9533|0.9754|0.9166|0.9999|0.9923|0.9677|0.9536|0.9811|0.9999|gnomAD_EAS|||||||||||||||||||-27|-2|23|25|0.00|0.00|0.00|0.00|PERM1,C|upstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000479361|retained_intron||||||||||rs13302983|2855|-1||SNV|HGNC|HGNC:28208|||1||||||||||||||0.9418|0.9539|0.999|0.9592|0.9847|||0.9721|0.9533|0.9754|0.9166|0.9999|0.9923|0.9677|0.9536|0.9811|0.9999|gnomAD_EAS|||||||||||||||||||-27|-2|23|25|0.00|0.00|0.00|0.00|PERM1,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000491024|protein_coding||||||||||rs13302983|3631|1|cds_start_NF|SNV|HGNC|HGNC:25284|||3|||ENSP00000462558||J3KSM5|UPI000268AE1F||||||||0.9418|0.9539|0.999|0.9592|0.9847|||0.9721|0.9533|0.9754|0.9166|0.9999|0.9923|0.9677|0.9536|0.9811|0.9999|gnomAD_EAS|||||||||||||||||||-27|-2|23|25|0.00|0.00|0.00|0.00|PERM1;Allele=C,C,C,C,C,C,C;Consequence=missense_variant,downstream_gene_variant,downstream_gene_variant,downstream_gene_variant,missense_variant,upstream_gene_variant,downstream_gene_variant;IMPACT=MODERATE,MODIFIER,MODIFIER,MODIFIER,MODERATE,MODIFIER,MODIFIER;SYMBOL=PERM1,PLEKHN1,PLEKHN1,PLEKHN1,PERM1,PERM1,PLEKHN1;Gene=ENSG00000187642,ENSG00000187583,ENSG00000187583,ENSG00000187583,ENSG00000187642,ENSG00000187642,ENSG00000187583;Feature_type=Transcript,Transcript,Transcript,Transcript,Transcript,Transcript,Transcript;Feature=ENST00000341290,ENST00000379407,ENST00000379409,ENST00000379410,ENST00000433179,ENST00000479361,ENST00000491024;BIOTYPE=protein_coding,protein_coding,protein_coding,protein_coding,protein_coding,retained_intron,protein_coding;EXON=3/5,.,.,.,1/3,.,.;INTRON=.,.,.,.,.,.,.;HGVSc=ENST00000341290.6:c.1192A>G,.,.,.,ENST00000433179.3:c.1534A>G,.,.;HGVSp=ENSP00000343864.2:p.Ser398Gly,.,.,.,ENSP00000414022.3:p.Ser512Gly,.,.;cDNA_position=1228,.,.,.,1534,.,.;CDS_position=1192,.,.,.,1534,.,.;Protein_position=398,.,.,.,512,.,.;Amino_acids=S/G,.,.,.,S/G,.,.;Codons=Agc/Ggc,.,.,.,Agc/Ggc,.,.;Existing_variation=rs13302983,rs13302983,rs13302983,rs13302983,rs13302983,rs13302983,rs13302983;DISTANCE=.,4488,4488,3631,.,2855,3631;STRAND=-1,1,1,1,-1,-1,1;FLAGS=.,.,.,.,.,.,cds_start_NF;VARIANT_CLASS=SNV,SNV,SNV,SNV,SNV,SNV,SNV;SYMBOL_SOURCE=HGNC,HGNC,HGNC,HGNC,HGNC,HGNC,HGNC;HGNC_ID=HGNC:28208,HGNC:25284,HGNC:25284,HGNC:25284,HGNC:28208,HGNC:28208,HGNC:25284;CANONICAL=.,.,.,YES,YES,.,.;MANE=.,.,.,NM_032129.3,.,.,.;TSL=2,1,2,1,5,1,3;APPRIS=A2,A2,A2,P3,P2,.,.;CCDS=.,CCDS53256.1,.,CCDS4.1,CCDS76083.1,.,.;ENSP=ENSP00000343864,ENSP00000368717,ENSP00000368719,ENSP00000368720,ENSP00000414022,.,ENSP00000462558;SWISSPROT=Q5SV97,Q494U1,Q494U1,Q494U1,Q5SV97,.,.;TREMBL=.,.,.,.,.,.,J3KSM5;UNIPARC=.,.,.,UPI00001416D8,.,.,UPI000268AE1F;GENE_PHENO=.,.,.,.,.,.,.;SIFT=tolerated(0.2),.,.,.,tolerated(0.18),.,.;PolyPhen=benign(0.003),.,.,.,benign(0.011),.,.;DOMAINS=PANTHER:PTHR47282&MobiDB_lite:mobidb-lite,.,.,.,PANTHER:PTHR47282&MobiDB_lite:mobidb-lite,.,.;miRNA=.,.,.,.,.,.,.;HGVS_OFFSET=.,.,.,.,.,.,.;AF=.,.,.,.,.,.,.;AFR_AF=0.9418,0.9418,0.9418,0.9418,0.9418,0.9418,0.9418;AMR_AF=0.9539,0.9539,0.9539,0.9539,0.9539,0.9539,0.9539;EAS_AF=0.999,0.999,0.999,0.999,0.999,0.999,0.999;EUR_AF=0.9592,0.9592,0.9592,0.9592,0.9592,0.9592,0.9592;SAS_AF=0.9847,0.9847,0.9847,0.9847,0.9847,0.9847,0.9847;AA_AF=.,.,.,.,.,.,.;EA_AF=.,.,.,.,.,.,.;gnomAD_AF=0.9721,0.9721,0.9721,0.9721,0.9721,0.9721,0.9721;gnomAD_AFR_AF=0.9533,0.9533,0.9533,0.9533,0.9533,0.9533,0.9533;gnomAD_AMR_AF=0.9754,0.9754,0.9754,0.9754,0.9754,0.9754,0.9754;gnomAD_ASJ_AF=0.9166,0.9166,0.9166,0.9166,0.9166,0.9166,0.9166;gnomAD_EAS_AF=0.9999,0.9999,0.9999,0.9999,0.9999,0.9999,0.9999;gnomAD_FIN_AF=0.9923,0.9923,0.9923,0.9923,0.9923,0.9923,0.9923;gnomAD_NFE_AF=0.9677,0.9677,0.9677,0.9677,0.9677,0.9677,0.9677;gnomAD_OTH_AF=0.9536,0.9536,0.9536,0.9536,0.9536,0.9536,0.9536;gnomAD_SAS_AF=0.9811,0.9811,0.9811,0.9811,0.9811,0.9811,0.9811;MAX_AF=0.9999,0.9999,0.9999,0.9999,0.9999,0.9999,0.9999;MAX_AF_POPS=gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS;CLIN_SIG=.,.,.,.,.,.,.;SOMATIC=.,.,.,.,.,.,.;PHENO=.,.,.,.,.,.,.;PUBMED=.,.,.,.,.,.,.;MOTIF_NAME=.,.,.,.,.,.,.;MOTIF_POS=.,.,.,.,.,.,.;HIGH_INF_POS=.,.,.,.,.,.,.;MOTIF_SCORE_CHANGE=.,.,.,.,.,.,.;existing_InFrame_oORFs=.,.,.,.,.,.,.;existing_OutOfFrame_oORFs=.,.,.,.,.,.,.;existing_uORFs=.,.,.,.,.,.,.;five_prime_UTR_variant_annotation=.,.,.,.,.,.,.;five_prime_UTR_variant_consequence=.,.,.,.,.,.,.;SpliceRegion=.,.,.,.,.,.,.;LoF=.,.,.,.,.,.,.;LoF_filter=.,.,.,.,.,.,.;LoF_flags=.,.,.,.,.,.,.;LoF_info=.,.,.,.,.,.,.;SpliceAI_pred_DP_AG=-27,-27,-27,-27,-27,-27,-27;SpliceAI_pred_DP_AL=-2,-2,-2,-2,-2,-2,-2;SpliceAI_pred_DP_DG=23,23,23,23,23,23,23;SpliceAI_pred_DP_DL=25,25,25,25,25,25,25;SpliceAI_pred_DS_AG=0,0,0,0,0,0,0;SpliceAI_pred_DS_AL=0,0,0,0,0,0,0;SpliceAI_pred_DS_DG=0,0,0,0,0,0,0;SpliceAI_pred_DS_DL=0,0,0,0,0,0,0;SpliceAI_pred_SYMBOL=PERM1,PERM1,PERM1,PERM1,PERM1,PERM1,PERM1
1	979560	.	T	C	.	.	CSQ=C|synonymous_variant|LOW|PERM1|ENSG00000187642|Transcript|ENST00000341290|protein_coding|3/5||ENST00000341290.6:c.1128A>G|ENSP00000343864.2:p.Ala376%3D|1164|1128|376|A|gcA/gcG|rs13303033||-1||SNV|HGNC|HGNC:28208|||2|A2||ENSP00000343864|Q5SV97||||||PANTHER:PTHR47282&Low_complexity_(Seg):seg|||0.5096|0.177|0.6095|0.7123|0.5895|0.5971|||0.5887|0.2428|0.6604|0.5617|0.7237|0.5334|0.5801|0.5647|0.6213|0.7237|gnomAD_EAS|||||||||||||||||||28|-30|-39|3|0.00|0.00|0.00|0.00|PERM1,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407|protein_coding||||||||||rs13303033|4552|1||SNV|HGNC|HGNC:25284|||1|A2|CCDS53256.1|ENSP00000368717|Q494U1|||||||||0.5096|0.177|0.6095|0.7123|0.5895|0.5971|||0.5887|0.2428|0.6604|0.5617|0.7237|0.5334|0.5801|0.5647|0.6213|0.7237|gnomAD_EAS|||||||||||||||||||28|-30|-39|3|0.00|0.00|0.00|0.00|PERM1,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409|protein_coding||||||||||rs13303033|4552|1||SNV|HGNC|HGNC:25284|||2|A2||ENSP00000368719|Q494U1|||||||||0.5096|0.177|0.6095|0.7123|0.5895|0.5971|||0.5887|0.2428|0.6604|0.5617|0.7237|0.5334|0.5801|0.5647|0.6213|0.7237|gnomAD_EAS|||||||||||||||||||28|-30|-39|3|0.00|0.00|0.00|0.00|PERM1,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410|protein_coding||||||||||rs13303033|3695|1||SNV|HGNC|HGNC:25284|YES|NM_032129.3|1|P3|CCDS4.1|ENSP00000368720|Q494U1||UPI00001416D8|||||||0.5096|0.177|0.6095|0.7123|0.5895|0.5971|||0.5887|0.2428|0.6604|0.5617|0.7237|0.5334|0.5801|0.5647|0.6213|0.7237|gnomAD_EAS|||||||||||||||||||28|-30|-39|3|0.00|0.00|0.00|0.00|PERM1,C|synonymous_variant|LOW|PERM1|ENSG00000187642|Transcript|ENST00000433179|protein_coding|1/3||ENST00000433179.3:c.1470A>G|ENSP00000414022.3:p.Ala490%3D|1470|1470|490|A|gcA/gcG|rs13303033||-1||SNV|HGNC|HGNC:28208|YES||5|P2|CCDS76083.1|ENSP00000414022|Q5SV97||||||PANTHER:PTHR47282&Low_complexity_(Seg):seg|||0.5096|0.177|0.6095|0.7123|0.5895|0.5971|||0.5887|0.2428|0.6604|0.5617|0.7237|0.5334|0.5801|0.5647|0.6213|0.7237|gnomAD_EAS|||||||||||||||||||28|-30|-39|3|0.00|0.00|0.00|0.00|PERM1,C|upstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000479361|retained_intron||||||||||rs13303033|2919|-1||SNV|HGNC|HGNC:28208|||1|||||||||||||0.5096|0.177|0.6095|0.7123|0.5895|0.5971|||0.5887|0.2428|0.6604|0.5617|0.7237|0.5334|0.5801|0.5647|0.6213|0.7237|gnomAD_EAS|||||||||||||||||||28|-30|-39|3|0.00|0.00|0.00|0.00|PERM1,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000491024|protein_coding||||||||||rs13303033|3695|1|cds_start_NF|SNV|HGNC|HGNC:25284|||3|||ENSP00000462558||J3KSM5|UPI000268AE1F|||||||0.5096|0.177|0.6095|0.7123|0.5895|0.5971|||0.5887|0.2428|0.6604|0.5617|0.7237|0.5334|0.5801|0.5647|0.6213|0.7237|gnomAD_EAS|||||||||||||||||||28|-30|-39|3|0.00|0.00|0.00|0.00|PERM1;Allele=C,C,C,C,C,C,C;Consequence=synonymous_variant,downstream_gene_variant,downstream_gene_variant,downstream_gene_variant,synonymous_variant,upstream_gene_variant,downstream_gene_variant;IMPACT=LOW,MODIFIER,MODIFIER,MODIFIER,LOW,MODIFIER,MODIFIER;SYMBOL=PERM1,PLEKHN1,PLEKHN1,PLEKHN1,PERM1,PERM1,PLEKHN1;Gene=ENSG00000187642,ENSG00000187583,ENSG00000187583,ENSG00000187583,ENSG00000187642,ENSG00000187642,ENSG00000187583;Feature_type=Transcript,Transcript,Transcript,Transcript,Transcript,Transcript,Transcript;Feature=ENST00000341290,ENST00000379407,ENST00000379409,ENST00000379410,ENST00000433179,ENST00000479361,ENST00000491024;BIOTYPE=protein_coding,protein_coding,protein_coding,protein_coding,protein_coding,retained_intron,protein_coding;EXON=3/5,.,.,.,1/3,.,.;INTRON=.,.,.,.,.,.,.;HGVSc=ENST00000341290.6:c.1128A>G,.,.,.,ENST00000433179.3:c.1470A>G,.,.;HGVSp=ENSP00000343864.2:p.Ala376%3D,.,.,.,ENSP00000414022.3:p.Ala490%3D,.,.;cDNA_position=1164,.,.,.,1470,.,.;CDS_position=1128,.,.,.,1470,.,.;Protein_position=376,.,.,.,490,.,.;Amino_acids=A,.,.,.,A,.,.;Codons=gcA/gcG,.,.,.,gcA/gcG,.,.;Existing_variation=rs13303033,rs13303033,rs13303033,rs13303033,rs13303033,rs13303033,rs13303033;DISTANCE=.,4552,4552,3695,.,2919,3695;STRAND=-1,1,1,1,-1,-1,1;FLAGS=.,.,.,.,.,.,cds_start_NF;VARIANT_CLASS=SNV,SNV,SNV,SNV,SNV,SNV,SNV;SYMBOL_SOURCE=HGNC,HGNC,HGNC,HGNC,HGNC,HGNC,HGNC;HGNC_ID=HGNC:28208,HGNC:25284,HGNC:25284,HGNC:25284,HGNC:28208,HGNC:28208,HGNC:25284;CANONICAL=.,.,.,YES,YES,.,.;MANE=.,.,.,NM_032129.3,.,.,.;TSL=2,1,2,1,5,1,3;APPRIS=A2,A2,A2,P3,P2,.,.;CCDS=.,CCDS53256.1,.,CCDS4.1,CCDS76083.1,.,.;ENSP=ENSP00000343864,ENSP00000368717,ENSP00000368719,ENSP00000368720,ENSP00000414022,.,ENSP00000462558;SWISSPROT=Q5SV97,Q494U1,Q494U1,Q494U1,Q5SV97,.,.;TREMBL=.,.,.,.,.,.,J3KSM5;UNIPARC=.,.,.,UPI00001416D8,.,.,UPI000268AE1F;GENE_PHENO=.,.,.,.,.,.,.;SIFT=.,.,.,.,.,.,.;PolyPhen=.,.,.,.,.,.,.;DOMAINS=PANTHER:PTHR47282&Low_complexity_(Seg):seg,.,.,.,PANTHER:PTHR47282&Low_complexity_(Seg):seg,.,.;miRNA=.,.,.,.,.,.,.;HGVS_OFFSET=.,.,.,.,.,.,.;AF=0.5096,0.5096,0.5096,0.5096,0.5096,0.5096,0.5096;AFR_AF=0.177,0.177,0.177,0.177,0.177,0.177,0.177;AMR_AF=0.6095,0.6095,0.6095,0.6095,0.6095,0.6095,0.6095;EAS_AF=0.7123,0.7123,0.7123,0.7123,0.7123,0.7123,0.7123;EUR_AF=0.5895,0.5895,0.5895,0.5895,0.5895,0.5895,0.5895;SAS_AF=0.5971,0.5971,0.5971,0.5971,0.5971,0.5971,0.5971;AA_AF=.,.,.,.,.,.,.;EA_AF=.,.,.,.,.,.,.;gnomAD_AF=0.5887,0.5887,0.5887,0.5887,0.5887,0.5887,0.5887;gnomAD_AFR_AF=0.2428,0.2428,0.2428,0.2428,0.2428,0.2428,0.2428;gnomAD_AMR_AF=0.6604,0.6604,0.6604,0.6604,0.6604,0.6604,0.6604;gnomAD_ASJ_AF=0.5617,0.5617,0.5617,0.5617,0.5617,0.5617,0.5617;gnomAD_EAS_AF=0.7237,0.7237,0.7237,0.7237,0.7237,0.7237,0.7237;gnomAD_FIN_AF=0.5334,0.5334,0.5334,0.5334,0.5334,0.5334,0.5334;gnomAD_NFE_AF=0.5801,0.5801,0.5801,0.5801,0.5801,0.5801,0.5801;gnomAD_OTH_AF=0.5647,0.5647,0.5647,0.5647,0.5647,0.5647,0.5647;gnomAD_SAS_AF=0.6213,0.6213,0.6213,0.6213,0.6213,0.6213,0.6213;MAX_AF=0.7237,0.7237,0.7237,0.7237,0.7237,0.7237,0.7237;MAX_AF_POPS=gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS;CLIN_SIG=.,.,.,.,.,.,.;SOMATIC=.,.,.,.,.,.,.;PHENO=.,.,.,.,.,.,.;PUBMED=.,.,.,.,.,.,.;MOTIF_NAME=.,.,.,.,.,.,.;MOTIF_POS=.,.,.,.,.,.,.;HIGH_INF_POS=.,.,.,.,.,.,.;MOTIF_SCORE_CHANGE=.,.,.,.,.,.,.;existing_InFrame_oORFs=.,.,.,.,.,.,.;existing_OutOfFrame_oORFs=.,.,.,.,.,.,.;existing_uORFs=.,.,.,.,.,.,.;five_prime_UTR_variant_annotation=.,.,.,.,.,.,.;five_prime_UTR_variant_consequence=.,.,.,.,.,.,.;SpliceRegion=.,.,.,.,.,.,.;LoF=.,.,.,.,.,.,.;LoF_filter=.,.,.,.,.,.,.;LoF_flags=.,.,.,.,.,.,.;LoF_info=.,.,.,.,.,.,.;SpliceAI_pred_DP_AG=28,28,28,28,28,28,28;SpliceAI_pred_DP_AL=-30,-30,-30,-30,-30,-30,-30;SpliceAI_pred_DP_DG=-39,-39,-39,-39,-39,-39,-39;SpliceAI_pred_DP_DL=3,3,3,3,3,3,3;SpliceAI_pred_DS_AG=0,0,0,0,0,0,0;SpliceAI_pred_DS_AL=0,0,0,0,0,0,0;SpliceAI_pred_DS_DG=0,0,0,0,0,0,0;SpliceAI_pred_DS_DL=0,0,0,0,0,0,0;SpliceAI_pred_SYMBOL=PERM1,PERM1,PERM1,PERM1,PERM1,PERM1,PERM1
1	999842	.	C	A	.	.	CSQ=A|intron_variant|MODIFIER|HES4|ENSG00000188290|Transcript|ENST00000304952|protein_coding||1/3|ENST00000304952.11:c.108+24G>T|||||||rs2298214||-1||SNV|HGNC|HGNC:24149||NM_021170.4|1|P1|CCDS5.1|ENSP00000304595|Q9HCC6|||||||||0.4938|0.0356|0.6268|0.7718|0.5895|0.6339|0.1386|0.5695|0.6136|0.1208|0.7139|0.6344|0.786|0.5555|0.595|0.5882|0.6625|0.786|gnomAD_EAS|||||||||||||||||||6|-37|6|24|0.00|0.00|0.01|0.02|HES4,A|missense_variant|MODERATE|HES4|ENSG00000188290|Transcript|ENST00000428771|protein_coding|1/3||ENST00000428771.6:c.132G>T|ENSP00000393198.2:p.Arg44Ser|331|132|44|R/S|agG/agT|rs2298214||-1||SNV|HGNC|HGNC:24149|YES||2||CCDS44034.1|ENSP00000393198||E9PB28|UPI0001881B51||tolerated_low_confidence(0.72)|benign(0)|MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg|||0.4938|0.0356|0.6268|0.7718|0.5895|0.6339|0.1386|0.5695|0.6136|0.1208|0.7139|0.6344|0.786|0.5555|0.595|0.5882|0.6625|0.786|gnomAD_EAS||||||||||||||||||MUTANT_DONOR_MES:11.0784944978449&EXON_END:1000172&INTRON_END:999691&DE_NOVO_DONOR_MES_POS:-156&DE_NOVO_DONOR_POS:-156&EXON_START:999692&DE_NOVO_DONOR_MES:7.0006176073036&DE_NOVO_DONOR_PROB:0.167156964545091&INTRON_START:999614|6|-37|6|24|0.00|0.00|0.01|0.02|HES4,A|non_coding_transcript_exon_variant|MODIFIER|HES4|ENSG00000188290|Transcript|ENST00000481869|retained_intron|1/2||ENST00000481869.1:n.255G>T||255|||||rs2298214||-1||SNV|HGNC|HGNC:24149|||2|||||||||||||0.4938|0.0356|0.6268|0.7718|0.5895|0.6339|0.1386|0.5695|0.6136|0.1208|0.7139|0.6344|0.786|0.5555|0.595|0.5882|0.6625|0.786|gnomAD_EAS|||||||||||||||||||6|-37|6|24|0.00|0.00|0.01|0.02|HES4,A|intron_variant|MODIFIER|HES4|ENSG00000188290|Transcript|ENST00000484667|protein_coding||1/2|ENST00000484667.2:c.108+24G>T|||||||rs2298214||-1||SNV|HGNC|HGNC:24149|||3|||ENSP00000425085||D6REB3|UPI0001D3BBEE|||||||0.4938|0.0356|0.6268|0.7718|0.5895|0.6339|0.1386|0.5695|0.6136|0.1208|0.7139|0.6344|0.786|0.5555|0.595|0.5882|0.6625|0.786|gnomAD_EAS|||||||||||||||||||6|-37|6|24|0.00|0.00|0.01|0.02|HES4,A|upstream_gene_variant|MODIFIER|AL645608.7|ENSG00000272512|Transcript|ENST00000606034|lncRNA||||||||||rs2298214|1791|-1||SNV|Clone_based_ensembl_gene||YES|||||||||||||||0.4938|0.0356|0.6268|0.7718|0.5895|0.6339|0.1386|0.5695|0.6136|0.1208|0.7139|0.6344|0.786|0.5555|0.595|0.5882|0.6625|0.786|gnomAD_EAS|||||||||||||||||||6|-37|6|24|0.00|0.00|0.01|0.02|HES4,A|upstream_gene_variant|MODIFIER|ISG15|ENSG00000187608|Transcript|ENST00000624652|protein_coding||||||||||rs2298214|1303|1|cds_end_NF|SNV|HGNC|HGNC:4053|||3|||ENSP00000485313||A0A096LNZ9||1||||||0.4938|0.0356|0.6268|0.7718|0.5895|0.6339|0.1386|0.5695|0.6136|0.1208|0.7139|0.6344|0.786|0.5555|0.595|0.5882|0.6625|0.786|gnomAD_EAS|||||||||||||||||||6|-37|6|24|0.00|0.00|0.01|0.02|HES4,A|upstream_gene_variant|MODIFIER|ISG15|ENSG00000187608|Transcript|ENST00000624697|protein_coding||||||||||rs2298214|1296|1||SNV|HGNC|HGNC:4053|||3|A2||ENSP00000485643||A0A096LPJ4||1||||||0.4938|0.0356|0.6268|0.7718|0.5895|0.6339|0.1386|0.5695|0.6136|0.1208|0.7139|0.6344|0.786|0.5555|0.595|0.5882|0.6625|0.786|gnomAD_EAS|||||||||||||||||||6|-37|6|24|0.00|0.00|0.01|0.02|HES4,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000118|promoter||||||||||rs2298214||||SNV||||||||||||||||||0.4938|0.0356|0.6268|0.7718|0.5895|0.6339|0.1386|0.5695|0.6136|0.1208|0.7139|0.6344|0.786|0.5555|0.595|0.5882|0.6625|0.786|gnomAD_EAS|||||||||||||||||||||||||||;Allele=A,A,A,A,A,A,A,A;Consequence=intron_variant,missense_variant,non_coding_transcript_exon_variant,intron_variant,upstream_gene_variant,upstream_gene_variant,upstream_gene_variant,regulatory_region_variant;IMPACT=MODIFIER,MODERATE,MODIFIER,MODIFIER,MODIFIER,MODIFIER,MODIFIER,MODIFIER;SYMBOL=HES4,HES4,HES4,HES4,AL645608.7,ISG15,ISG15,.;Gene=ENSG00000188290,ENSG00000188290,ENSG00000188290,ENSG00000188290,ENSG00000272512,ENSG00000187608,ENSG00000187608,.;Feature_type=Transcript,Transcript,Transcript,Transcript,Transcript,Transcript,Transcript,RegulatoryFeature;Feature=ENST00000304952,ENST00000428771,ENST00000481869,ENST00000484667,ENST00000606034,ENST00000624652,ENST00000624697,ENSR00000000118;BIOTYPE=protein_coding,protein_coding,retained_intron,protein_coding,lncRNA,protein_coding,protein_coding,promoter;EXON=.,1/3,1/2,.,.,.,.,.;INTRON=1/3,.,.,1/2,.,.,.,.;HGVSc=ENST00000304952.11:c.108+24G>T,ENST00000428771.6:c.132G>T,ENST00000481869.1:n.255G>T,ENST00000484667.2:c.108+24G>T,.,.,.,.;HGVSp=.,ENSP00000393198.2:p.Arg44Ser,.,.,.,.,.,.;cDNA_position=.,331,255,.,.,.,.,.;CDS_position=.,132,.,.,.,.,.,.;Protein_position=.,44,.,.,.,.,.,.;Amino_acids=.,R/S,.,.,.,.,.,.;Codons=.,agG/agT,.,.,.,.,.,.;Existing_variation=rs2298214,rs2298214,rs2298214,rs2298214,rs2298214,rs2298214,rs2298214,rs2298214;DISTANCE=.,.,.,.,1791,1303,1296,.;STRAND=-1,-1,-1,-1,-1,1,1,.;FLAGS=.,.,.,.,.,cds_end_NF,.,.;VARIANT_CLASS=SNV,SNV,SNV,SNV,SNV,SNV,SNV,SNV;SYMBOL_SOURCE=HGNC,HGNC,HGNC,HGNC,Clone_based_ensembl_gene,HGNC,HGNC,.;HGNC_ID=HGNC:24149,HGNC:24149,HGNC:24149,HGNC:24149,.,HGNC:4053,HGNC:4053,.;CANONICAL=.,YES,.,.,YES,.,.,.;MANE=NM_021170.4,.,.,.,.,.,.,.;TSL=1,2,2,3,.,3,3,.;APPRIS=P1,.,.,.,.,.,A2,.;CCDS=CCDS5.1,CCDS44034.1,.,.,.,.,.,.;ENSP=ENSP00000304595,ENSP00000393198,.,ENSP00000425085,.,ENSP00000485313,ENSP00000485643,.;SWISSPROT=Q9HCC6,.,.,.,.,.,.,.;TREMBL=.,E9PB28,.,D6REB3,.,A0A096LNZ9,A0A096LPJ4,.;UNIPARC=.,UPI0001881B51,.,UPI0001D3BBEE,.,.,.,.;GENE_PHENO=.,.,.,.,.,1,1,.;SIFT=.,tolerated_low_confidence(0.72),.,.,.,.,.,.;PolyPhen=.,benign(0),.,.,.,.,.,.;DOMAINS=.,MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg,.,.,.,.,.,.;miRNA=.,.,.,.,.,.,.,.;HGVS_OFFSET=.,.,.,.,.,.,.,.;AF=0.4938,0.4938,0.4938,0.4938,0.4938,0.4938,0.4938,0.4938;AFR_AF=0.0356,0.0356,0.0356,0.0356,0.0356,0.0356,0.0356,0.0356;AMR_AF=0.6268,0.6268,0.6268,0.6268,0.6268,0.6268,0.6268,0.6268;EAS_AF=0.7718,0.7718,0.7718,0.7718,0.7718,0.7718,0.7718,0.7718;EUR_AF=0.5895,0.5895,0.5895,0.5895,0.5895,0.5895,0.5895,0.5895;SAS_AF=0.6339,0.6339,0.6339,0.6339,0.6339,0.6339,0.6339,0.6339;AA_AF=0.1386,0.1386,0.1386,0.1386,0.1386,0.1386,0.1386,0.1386;EA_AF=0.5695,0.5695,0.5695,0.5695,0.5695,0.5695,0.5695,0.5695;gnomAD_AF=0.6136,0.6136,0.6136,0.6136,0.6136,0.6136,0.6136,0.6136;gnomAD_AFR_AF=0.1208,0.1208,0.1208,0.1208,0.1208,0.1208,0.1208,0.1208;gnomAD_AMR_AF=0.7139,0.7139,0.7139,0.7139,0.7139,0.7139,0.7139,0.7139;gnomAD_ASJ_AF=0.6344,0.6344,0.6344,0.6344,0.6344,0.6344,0.6344,0.6344;gnomAD_EAS_AF=0.786,0.786,0.786,0.786,0.786,0.786,0.786,0.786;gnomAD_FIN_AF=0.5555,0.5555,0.5555,0.5555,0.5555,0.5555,0.5555,0.5555;gnomAD_NFE_AF=0.595,0.595,0.595,0.595,0.595,0.595,0.595,0.595;gnomAD_OTH_AF=0.5882,0.5882,0.5882,0.5882,0.5882,0.5882,0.5882,0.5882;gnomAD_SAS_AF=0.6625,0.6625,0.6625,0.6625,0.6625,0.6625,0.6625,0.6625;MAX_AF=0.786,0.786,0.786,0.786,0.786,0.786,0.786,0.786;MAX_AF_POPS=gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS,gnomAD_EAS;CLIN_SIG=.,.,.,.,.,.,.,.;SOMATIC=.,.,.,.,.,.,.,.;PHENO=.,.,.,.,.,.,.,.;PUBMED=.,.,.,.,.,.,.,.;MOTIF_NAME=.,.,.,.,.,.,.,.;MOTIF_POS=.,.,.,.,.,.,.,.;HIGH_INF_POS=.,.,.,.,.,.,.,.;MOTIF_SCORE_CHANGE=.,.,.,.,.,.,.,.;existing_InFrame_oORFs=.,.,.,.,.,.,.,.;existing_OutOfFrame_oORFs=.,.,.,.,.,.,.,.;existing_uORFs=.,.,.,.,.,.,.,.;five_prime_UTR_variant_annotation=.,.,.,.,.,.,.,.;five_prime_UTR_variant_consequence=.,.,.,.,.,.,.,.;SpliceRegion=.,.,.,.,.,.,.,.;LoF=.,.,.,.,.,.,.,.;LoF_filter=.,.,.,.,.,.,.,.;LoF_flags=.,.,.,.,.,.,.,.;LoF_info=.,MUTANT_DONOR_MES:11.0784944978449&EXON_END:1000172&INTRON_END:999691&DE_NOVO_DONOR_MES_POS:-156&DE_NOVO_DONOR_POS:-156&EXON_START:999692&DE_NOVO_DONOR_MES:7.0006176073036&DE_NOVO_DONOR_PROB:0.167156964545091&INTRON_START:999614,.,.,.,.,.,.;SpliceAI_pred_DP_AG=6,6,6,6,6,6,6,.;SpliceAI_pred_DP_AL=-37,-37,-37,-37,-37,-37,-37,.;SpliceAI_pred_DP_DG=6,6,6,6,6,6,6,.;SpliceAI_pred_DP_DL=24,24,24,24,24,24,24,.;SpliceAI_pred_DS_AG=0,0,0,0,0,0,0,.;SpliceAI_pred_DS_AL=0,0,0,0,0,0,0,.;SpliceAI_pred_DS_DG=0.01,0.01,0.01,0.01,0.01,0.01,0.01,.;SpliceAI_pred_DS_DL=0.02,0.02,0.02,0.02,0.02,0.02,0.02,.;SpliceAI_pred_SYMBOL=HES4,HES4,HES4,HES4,HES4,HES4,HES4,.
1	12716215	.	C	A	.	.	CSQ=A|stop_gained|HIGH|AADACL3|ENSG00000188984|Transcript|ENST00000359318|protein_coding|1/4||ENST00000359318.8:c.39C>A|ENSP00000352268.6:p.Cys13Ter|106|39|13|C/*|tgC/tgA|rs3000860||1||SNV|HGNC|HGNC:32037|YES|NM_001103170.3|3|P1|CCDS41253.2|ENSP00000352268|Q5VUY0||UPI0003EAEC70||||PIRSF:PIRSF037251&PANTHER:PTHR23024&PANTHER:PTHR23024:SF115&Transmembrane_helices:TMhelix|||0.1436|0.1188|0.1052|0.2679|0.1362|0.0838||||||||||||0.2679|EAS|||||||||||||||HC|||GERP_DIST:92.57575&BP_DIST:1182&PERCENTILE:0.0318627450980392&DIST_FROM_LAST_EXON:408&50_BP_RULE:PASS&PHYLOCSF_TOO_SHORT|||||||||,A|non_coding_transcript_exon_variant|MODIFIER|AADACL3|ENSG00000188984|Transcript|ENST00000620146|processed_transcript|1/3||ENST00000620146.2:n.101C>A||101|||||rs3000860||1||SNV|HGNC|HGNC:32037|||2|||||||||||||0.1436|0.1188|0.1052|0.2679|0.1362|0.0838||||||||||||0.2679|EAS|||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000347677|promoter_flanking_region||||||||||rs3000860||||SNV||||||||||||||||||0.1436|0.1188|0.1052|0.2679|0.1362|0.0838||||||||||||0.2679|EAS|||||||||||||||||||||||||||;Allele=A,A,A;Consequence=stop_gained,non_coding_transcript_exon_variant,regulatory_region_variant;IMPACT=HIGH,MODIFIER,MODIFIER;SYMBOL=AADACL3,AADACL3,.;Gene=ENSG00000188984,ENSG00000188984,.;Feature_type=Transcript,Transcript,RegulatoryFeature;Feature=ENST00000359318,ENST00000620146,ENSR00000347677;BIOTYPE=protein_coding,processed_transcript,promoter_flanking_region;EXON=1/4,1/3,.;INTRON=.,.,.;HGVSc=ENST00000359318.8:c.39C>A,ENST00000620146.2:n.101C>A,.;HGVSp=ENSP00000352268.6:p.Cys13Ter,.,.;cDNA_position=106,101,.;CDS_position=39,.,.;Protein_position=13,.,.;Amino_acids=C/*,.,.;Codons=tgC/tgA,.,.;Existing_variation=rs3000860,rs3000860,rs3000860;DISTANCE=.,.,.;STRAND=1,1,.;FLAGS=.,.,.;VARIANT_CLASS=SNV,SNV,SNV;SYMBOL_SOURCE=HGNC,HGNC,.;HGNC_ID=HGNC:32037,HGNC:32037,.;CANONICAL=YES,.,.;MANE=NM_001103170.3,.,.;TSL=3,2,.;APPRIS=P1,.,.;CCDS=CCDS41253.2,.,.;ENSP=ENSP00000352268,.,.;SWISSPROT=Q5VUY0,.,.;TREMBL=.,.,.;UNIPARC=UPI0003EAEC70,.,.;GENE_PHENO=.,.,.;SIFT=.,.,.;PolyPhen=.,.,.;DOMAINS=PIRSF:PIRSF037251&PANTHER:PTHR23024&PANTHER:PTHR23024:SF115&Transmembrane_helices:TMhelix,.,.;miRNA=.,.,.;HGVS_OFFSET=.,.,.;AF=0.1436,0.1436,0.1436;AFR_AF=0.1188,0.1188,0.1188;AMR_AF=0.1052,0.1052,0.1052;EAS_AF=0.2679,0.2679,0.2679;EUR_AF=0.1362,0.1362,0.1362;SAS_AF=0.0838,0.0838,0.0838;AA_AF=.,.,.;EA_AF=.,.,.;gnomAD_AF=.,.,.;gnomAD_AFR_AF=.,.,.;gnomAD_AMR_AF=.,.,.;gnomAD_ASJ_AF=.,.,.;gnomAD_EAS_AF=.,.,.;gnomAD_FIN_AF=.,.,.;gnomAD_NFE_AF=.,.,.;gnomAD_OTH_AF=.,.,.;gnomAD_SAS_AF=.,.,.;MAX_AF=0.2679,0.2679,0.2679;MAX_AF_POPS=EAS,EAS,EAS;CLIN_SIG=.,.,.;SOMATIC=.,.,.;PHENO=.,.,.;PUBMED=.,.,.;MOTIF_NAME=.,.,.;MOTIF_POS=.,.,.;HIGH_INF_POS=.,.,.;MOTIF_SCORE_CHANGE=.,.,.;existing_InFrame_oORFs=.,.,.;existing_OutOfFrame_oORFs=.,.,.;existing_uORFs=.,.,.;five_prime_UTR_variant_annotation=.,.,.;five_prime_UTR_variant_consequence=.,.,.;SpliceRegion=.,.,.;LoF=HC,.,.;LoF_filter=.,.,.;LoF_flags=.,.,.;LoF_info=GERP_DIST:92.57575&BP_DIST:1182&PERCENTILE:0.0318627450980392&DIST_FROM_LAST_EXON:408&50_BP_RULE:PASS&PHYLOCSF_TOO_SHORT,.,.;SpliceAI_pred_DP_AG=.,.,.;SpliceAI_pred_DP_AL=.,.,.;SpliceAI_pred_DP_DG=.,.,.;SpliceAI_pred_DP_DL=.,.,.;SpliceAI_pred_DS_AG=.,.,.;SpliceAI_pred_DS_AL=.,.,.;SpliceAI_pred_DS_DG=.,.,.;SpliceAI_pred_DS_DL=.,.,.;SpliceAI_pred_SYMBOL=.,.,.