ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.1119-18C>G

gnomAD frequency: 0.00053  dbSNP: rs367960459
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000781725 SCV000919994 uncertain significance not specified 2018-02-26 criteria provided, single submitter clinical testing Variant summary: PKHD1 c.1119-18C>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. Two predict the variant creates a cryptic donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0002 in 276526 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in PKHD1 causing Polycystic Kidney and Hepatic Disease (0.0002 vs 0.0071), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.1119-18C>G in individuals affected with Polycystic Kidney and Hepatic Disease and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.
Invitae RCV002067384 SCV002338695 likely benign Autosomal recessive polycystic kidney disease 2024-01-31 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003908087 SCV004720932 likely benign PKHD1-related condition 2022-05-31 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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