ClinVar Miner

Submissions for variant NM_138694.4(PKHD1):c.7587G>A (p.Gly2529=) (rs12210295)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000082571 SCV000114613 benign not specified 2015-10-27 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000082571 SCV000315827 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000273935 SCV000464062 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000082571 SCV000592900 benign not specified 2016-05-11 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589950 SCV000699876 benign not provided 2016-07-11 criteria provided, single submitter clinical testing Variant summary: The c.7587G>A (p.Gly2529=) in PKHD1 gene is a synonymous change that involves a non-conserved nucleotide with 4/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.506 (61140/120660 chrs tested) including numerous homozygous occurrences. This frequency greatly exceeds the maximal expected frequency of a pathogenic allele (0.007) in this gene. The variant of interest was cited as Benign by a reputable clinical laboratory. It is widely accepted as a rare polymorphism in the field. Taking together, the variant was classified as Benign.
Invitae RCV000273935 SCV001000019 benign Autosomal recessive polycystic kidney disease 2019-12-31 criteria provided, single submitter clinical testing

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