ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.9829+10T>G

gnomAD frequency: 0.00518  dbSNP: rs143526199
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000153704 SCV000203262 benign not specified 2014-01-14 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001081953 SCV000291345 benign Autosomal recessive polycystic kidney disease 2024-01-31 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000153704 SCV000315855 benign not specified criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000587786 SCV000699889 benign not provided 2016-04-26 criteria provided, single submitter clinical testing Variant summary: The PKHD1 c.9829+10T>G variant affects a non-conserved intronic nucleotide. Mutation Taster predicts benign outcome for this variant, and 5/5/ in silico tools via Alamut predict no significant change to splicing. Functional studies have not been carried out to confirm these in silico predictions. This variant was found in 199/121356 control chromosomes at a frequency of 0.0016398,predominantly in individuals of African descent (1.65%), including 2 homozygous occurrences. This frequency exceeds the maximal expected allele frequency for a pathogenic variant in PKHD1 gene (0.7%). The variant has been reported as a polymorphism identified in controls, and has been reported in only one ARPKD patient without evidence of causality (i.e. co-segregation). Additionally, one clinical lab has classified the variant as benign. Taken together, the variant was classified as benign.
Illumina Laboratory Services, Illumina RCV001081953 SCV001324923 likely benign Autosomal recessive polycystic kidney disease 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000587786 SCV001812317 likely benign not provided 2019-02-04 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000587786 SCV005226123 likely benign not provided criteria provided, single submitter not provided
Natera, Inc. RCV001081953 SCV002075535 benign Autosomal recessive polycystic kidney disease 2017-05-11 no assertion criteria provided clinical testing

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