ClinVar Miner

Submissions for variant NM_004484.3(GPC3):c.1626A>G (p.Ala542=) (rs61754631)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000125253 SCV000168694 benign not specified 2014-04-11 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
PreventionGenetics,PreventionGenetics RCV000125253 SCV000310403 benign not specified criteria provided, single submitter clinical testing
Invitae RCV000470318 SCV000559601 benign Wilms tumor 1 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586499 SCV000698457 benign not provided 2016-05-05 criteria provided, single submitter clinical testing Variant summary: The GPC3 variant, c.1626A>G (p.Ala542Ala) causes a synonymous change involving a non-conserved nucleotide with 5/5 in silico tools via Alamut predicting no significant effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 1792/87714 (1/48, 141 homozygotes, 396 hemizygotes), which significantly exceeds the estimated maxium expected allele frequency for a pathogenic GPC3 variant of 1/10000000. The variant of interest, to our knowledge, has not been reported in affected individuals via publications. A reputable clinical laboratory cites the variant as "benign." Therefore, the variant of interest is classified as Benign.
Ambry Genetics RCV000716283 SCV000847123 benign History of neurodevelopmental disorder 2015-10-12 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance

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