diff --git a/v03_pipeline/lib/model/dataset_type.py b/v03_pipeline/lib/model/dataset_type.py index f89cffb92..f19cb7432 100644 --- a/v03_pipeline/lib/model/dataset_type.py +++ b/v03_pipeline/lib/model/dataset_type.py @@ -373,6 +373,10 @@ def should_send_to_allele_registry(self): def requires_dataproc(self): return self == DatasetType.SNV_INDEL + @property + def filter_invalid_sites(self): + return self == DatasetType.SNV_INDEL + @property def should_export_to_vcf(self): return self == DatasetType.SV diff --git a/v03_pipeline/lib/reference_datasets/clinvar.py b/v03_pipeline/lib/reference_datasets/clinvar.py index 837742d1c..3ed325eab 100644 --- a/v03_pipeline/lib/reference_datasets/clinvar.py +++ b/v03_pipeline/lib/reference_datasets/clinvar.py @@ -154,10 +154,13 @@ def select_fields(ht): conflictingPathogenicities=parsed_and_mapped_clnsigconf(ht), goldStars=CLINVAR_GOLD_STARS_LOOKUP.get(hl.delimit(ht.info.CLNREVSTAT)), submitters=ht.submitters, - # assumes the format 'MedGen#:condition', e.g.'C0023264:Leigh syndrome' - conditions=hl.map( - lambda p: p.split(r':')[1], - ht.conditions, + # assumes the format 'MedGen#:condition;MedGen#:condition', e.g.'C0023264:Leigh syndrome' + conditions=hl.filter( + hl.is_defined, + hl.flatmap( + lambda p: p.split(';'), + ht.conditions, + ).map(lambda p: p.split(':')[1]), ), ) diff --git a/v03_pipeline/lib/reference_datasets/clinvar_test.py b/v03_pipeline/lib/reference_datasets/clinvar_test.py index e62e34e2d..9810cb578 100644 --- a/v03_pipeline/lib/reference_datasets/clinvar_test.py +++ b/v03_pipeline/lib/reference_datasets/clinvar_test.py @@ -169,3 +169,73 @@ def test_get_ht(self): ), ], ) + + # VariationID 9 tests Conditions parsing + self.assertListEqual( + ht.collect()[8].submitters, + [ + 'Hemochromatosis type 1', + 'Hereditary cancer-predisposing syndrome', + 'HFE-related disorder', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Bronze diabetes', + 'Hemochromatosis type 1', + 'HFE-related disorder', + 'Hemochromatosis type 1', + 'Abdominal pain', + 'Atypical behavior', + 'Pain', + 'Peripheral neuropathy', + 'Abnormality of the nervous system', + 'Abnormality of the male genitalia', + 'Abnormal peripheral nervous system morphology', + 'Hereditary hemochromatosis', + 'Hemochromatosis type 1', + 'not provided', + 'Hereditary hemochromatosis', + 'not provided', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'not provided', + 'not provided', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Hereditary hemochromatosis', + 'Cardiomyopathy', + 'not provided', + 'Juvenile hemochromatosis', + 'Hemochromatosis type 1', + 'not provided', + 'not provided', + 'Inborn genetic diseases', + 'Hemochromatosis type 1', + 'not provided', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'not provided', + 'Porphyrinuria', + 'Cutaneous photosensitivity', + 'Hemochromatosis type 1', + 'Hereditary hemochromatosis', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + 'not provided', + 'Hemochromatosis type 1', + 'Variegate porphyria', + 'Familial porphyria cutanea tarda', + 'Alzheimer disease type 1', + 'Microvascular complications of diabetes, susceptibility to, 7', + 'Transferrin serum level quantitative trait locus 2', + 'Hemochromatosis type 1', + 'Hemochromatosis type 1', + ], + ) diff --git a/v03_pipeline/lib/tasks/validate_callset.py b/v03_pipeline/lib/tasks/validate_callset.py index 8d4ff674c..e8f5d6f34 100644 --- a/v03_pipeline/lib/tasks/validate_callset.py +++ b/v03_pipeline/lib/tasks/validate_callset.py @@ -26,6 +26,8 @@ WriteValidationErrorsForRunTask, ) +MAX_SNV_INDEL_ALLELE_LENGTH = 500 + @luigi.util.inherits(BaseLoadingRunParams) class ValidateCallsetTask(BaseUpdateTask): @@ -71,14 +73,20 @@ def update_table(self, mt: hl.MatrixTable) -> hl.MatrixTable: self.callset_path, ), ) - if self.dataset_type.can_run_validation: - # Rather than throwing an error, we silently remove invalid contigs. - # This happens fairly often for AnVIL requests. + if self.dataset_type.filter_invalid_sites: mt = mt.filter_rows( - hl.set(self.reference_genome.standard_contigs).contains( - mt.locus.contig, + ( + # Rather than throwing an error, we silently remove invalid contigs. + # This happens fairly often for AnVIL requests. + hl.set(self.reference_genome.standard_contigs).contains( + mt.locus.contig, + ) + # DRAGEN callsets produce long alternate alleles + # that aren't particularly analyzable as INDELs. + & (hl.len(mt.alleles[1]) < MAX_SNV_INDEL_ALLELE_LENGTH) ), ) + validation_exceptions = [] if self.skip_validation or not self.dataset_type.can_run_validation: return mt.select_globals( diff --git a/v03_pipeline/var/test/callsets/1kg_30variants.vcf b/v03_pipeline/var/test/callsets/1kg_30variants.vcf index 71070ea43..c92e9b642 100644 --- a/v03_pipeline/var/test/callsets/1kg_30variants.vcf +++ b/v03_pipeline/var/test/callsets/1kg_30variants.vcf @@ -155,4 +155,5 @@ 1 902024 rs181910588 G A 406.47 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-3.35500e+00;DB;DP=225;Dels=0.00000e+00;FS=1.03150e+01;HaplotypeScore=3.56800e-01;InbreedingCoeff=-1.33000e-02;MQ=5.93500e+01;MQ0=0;MQRankSum=1.21200e+00;QD=1.09900e+01;ReadPosRankSum=-1.50700e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=6.64000e+00;culprit=InbreedingCoeff;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs181910588|1|4231|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs181910588|1|2114|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs181910588|1|929|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs181910588|1|4166|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs181910588|1|2480|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs181910588|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.83+30N>A||A:0.0023|A:0.01||||A:0.001842|A:0||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs181910588|1||||||regulatory_region|||||||||||||||A:0.0023|A:0.01||||A:0.001842|A:0||||||||||||||||| GT:AD:DP:GQ:PL 0/0:18,0:18:54:0,54,689 0/0:21,0:21:63:0,63,797 0/0:17,0:17:48:0,48,608 0/0:5,0:5:15:0,15,182 0/0:9,0:9:27:0,27,333 0/0:7,0:7:21:0,21,253 0/0:18,0:18:54:0,54,680 0/0:7,0:7:21:0,21,259 0/0:17,0:17:51:0,51,614 0/0:19,0:19:54:0,54,647 0/0:20,0:20:60:0,60,756 0/0:14,0:14:42:0,42,518 0/0:13,0:13:36:0,36,466 0/0:14,0:14:42:0,42,535 0/1:9,1:11:4:4,0,296 0/0:15,0:15:45:0,45,551 1 902069 rs116147894 T C 13024.04 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=2.08840e+01;DB;DP=157;Dels=0.00000e+00;FS=3.07700e+00;HaplotypeScore=2.10500e-01;InbreedingCoeff=1.00200e-01;MQ=5.91800e+01;MQ0=0;MQRankSum=7.75000e-01;QD=1.56200e+01;ReadPosRankSum=-5.68400e+00;SNPEFF_EFFECT=DOWNSTREAM;SNPEFF_FUNCTIONAL_CLASS=NONE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=KLHL17;SNPEFF_IMPACT=MODIFIER;SNPEFF_TRANSCRIPT_ID=ENST00000338591;VQSLOD=7.17000e+00;culprit=MQ;CSQ=C|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs116147894|1|4186|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs116147894|1|2159|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs116147894|1|974|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||EXON_INTRON_UNDEF|||||||,C|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs116147894|1|4211|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379409|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06||||1/14||ENST00000379409.2:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187583|ENST00000379407|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF||||1/14||ENST00000379407.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs116147894|1|2525|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163|||||||||||||||||,C|ENSG00000187583|ENST00000379410|Transcript|intron_variant||||||rs116147894|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8||||1/15||ENST00000379410.3:c.84-15N>C||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||INTRON_SIZE:89||NON_CAN_SPLICE|||||||,C||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs116147894|1||||||regulatory_region|||||||||||||||C:0.0808|C:0.17|C:0.07|C:0.07|C:0.03|C:0.112713|C:0.017163||||||||||||||||| GT:AD:DP:GQ:PL 0/0:10,0:10:30:0,30,367 0/1:12,2:13:3:3,0,418 0/0:14,0:14:42:0,42,514 0/0:4,0:4:12:0,12,144 0/0:5,0:5:15:0,15,176 0/0:4,0:4:12:0,12,145 0/0:17,0:17:48:0,48,603 0/0:6,0:6:18:0,18,227 0/0:10,0:10:30:0,30,361 0/0:10,0:10:30:0,30,372 0/0:12,0:12:36:0,36,434 0/0:7,0:7:21:0,21,259 0/0:7,0:7:21:0,21,255 0/0:11,0:11:30:0,30,375 0/0:12,0:12:36:0,36,426 0/0:15,0:15:45:0,45,530 1 902088 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 +1 902088 . G ACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACTACT 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540 GL000207.1 1 . G A 324.34 PASS AC=1;AF=3.10000e-02;AN=32;BaseQRankSum=-5.34900e+00;DP=133;Dels=0.00000e+00;FS=7.94000e-01;HaplotypeScore=1.50400e-01;InbreedingCoeff=3.03000e-02;MQ=5.93200e+01;MQ0=0;MQRankSum=2.32200e+00;QD=7.91000e+00;ReadPosRankSum=-2.12100e+00;SNPEFF_AMINO_ACID_CHANGE=D30N;SNPEFF_CODON_CHANGE=Gac/Aac;SNPEFF_EFFECT=NON_SYNONYMOUS_CODING;SNPEFF_EXON_ID=exon_1_902084_902183;SNPEFF_FUNCTIONAL_CLASS=MISSENSE;SNPEFF_GENE_BIOTYPE=protein_coding;SNPEFF_GENE_NAME=PLEKHN1;SNPEFF_IMPACT=MODERATE;SNPEFF_TRANSCRIPT_ID=ENST00000379407;VQSLOD=5.23000e+00;culprit=QD;CSQ=A|ENSG00000187583|ENST00000480267|Transcript|upstream_gene_variant||||||rs201730138|1|4167|1|PLEKHN1|HGNC|25284|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000466300|Transcript|downstream_gene_variant||||||rs201730138|1|2178|1|KLHL17|HGNC|24023|nonsense_mediated_decay||||ENSP00000463694|||UPI000268AE1E||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187961|ENST00000338591|Transcript|downstream_gene_variant||||||rs201730138|1|993|1|KLHL17|HGNC|24023|protein_coding|YES||CCDS30550.1|ENSP00000343930|KLH17_HUMAN|Q0VGE6_HUMAN&B3KXL7_HUMAN|UPI00001DFBF0||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||EXON_INTRON_UNDEF|||||||,A|ENSG00000187961|ENST00000463212|Transcript|downstream_gene_variant||||||rs201730138|1|4230|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379409|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding||||ENSP00000368719|PKHN1_HUMAN|J3KSM5_HUMAN|UPI0000D61E06|tolerated(0.26)|benign(0.034)|2/15|||ENST00000379409.2:c.88N>A|ENSP00000368719.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0441767068273092||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187583|ENST00000379407|Transcript|missense_variant|118|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|||CCDS53256.1|ENSP00000368717|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00005764FF|tolerated(0.25)|benign(0.072)|2/15|||ENST00000379407.3:c.88N>A|ENSP00000368717.2:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0508376660889659||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A|ENSG00000187961|ENST00000481067|Transcript|downstream_gene_variant||||||rs201730138|1|2544|1|KLHL17|HGNC|24023|retained_intron|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600|||||||||||||||||,A|ENSG00000187583|ENST00000379410|Transcript|missense_variant|123|88|30|D/N|Gac/Aac|rs201730138|1||1|PLEKHN1|HGNC|25284|protein_coding|YES||CCDS4.1|ENSP00000368720|PKHN1_HUMAN|J3KSM5_HUMAN|UPI00001416D8|tolerated(0.25)|benign(0.072)|2/16|||ENST00000379410.3:c.88N>A|ENSP00000368720.3:p.Asp30Asn|A:0.0005||A:0.0028|||A:0|A:0.000600||||||||POSITION:0.0479302832244009||NON_CAN_SPLICE_SURR||B%3BB%3BB|15.10|D|T|T%3BT%3BT|T%3BT%3BT,A||ENSR00000528862|RegulatoryFeature|regulatory_region_variant||||||rs201730138|1||||||regulatory_region|||||||||||||||A:0.0005||A:0.0028|||A:0|A:0.000600||||||||||||||||| GT:AD:DP:GQ:PL 0/1:10,1:11:1:1,0,264 0/0:13,0:13:33:0,33,447 0/0:10,0:10:30:0,30,371 0/0:4,0:4:12:0,12,141 0/0:1,0:1:3:0,3,39 0/0:4,0:4:12:0,12,145 0/0:18,0:18:51:0,51,665 0/0:4,0:4:12:0,12,148 0/0:5,0:5:15:0,15,193 0/0:9,0:9:24:0,24,320 0/0:10,0:10:30:0,30,378 0/0:4,0:4:12:0,12,160 0/0:10,0:10:30:0,30,387 0/0:7,0:7:21:0,21,247 0/0:9,0:9:27:0,27,350 0/0:14,0:14:42:0,42,540