ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.318C>T (p.Arg106=) (rs762542246)

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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 RCV000724466 SCV000227029 uncertain significance not provided 2016-12-02 criteria provided, single submitter clinical testing
Invitae RCV001248965 SCV000626598 benign Glycogen storage disease, type II 2019-12-31 criteria provided, single submitter clinical testing
GeneDx RCV000724466 SCV000725429 likely benign not provided 2018-12-28 criteria provided, single submitter clinical testing
Pars Genome Lab RCV001248965 SCV001652864 likely benign Glycogen storage disease, type II 2021-05-18 criteria provided, single submitter clinical testing
Nilou-Genome Lab RCV001248965 SCV001810229 likely benign Glycogen storage disease, type II 2021-07-22 criteria provided, single submitter clinical testing
Broad Institute Rare Disease Group, Broad Institute RCV001248965 SCV001422771 likely benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The c.318C>T (p.Arg106=) variant in GAA has not been previously reported in individuals with Glycogen Storage Disease II but has been reported as a VUS by EGL Genetic Diagnostics, a likely benign variant by GeneDx, and a benign variant by Invitae in ClinVar (Variation ID: 195019). This variant has been identified in 0.010% (13/126514) of European (non-Finnish) chromosomes, including 2 homozygotes, by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs762542246). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Computational prediction tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. However, novel synonymous variants supported by computational evidence without raised suspicion for an impact are likely benign (Richards 2015). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely benign. ACMG/AMP Criteria applied: PM2, BP4, BP7 (Richards 2015).

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