ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.1416C>T (p.Thr472=) (rs368492669)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001087314 SCV000626510 likely benign Glycogen storage disease, type II 2020-12-03 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000727406 SCV000708270 uncertain significance not provided 2017-05-04 criteria provided, single submitter clinical testing
GeneDx RCV000727406 SCV000727626 likely benign not provided 2019-02-28 criteria provided, single submitter clinical testing
Nilou-Genome Lab RCV001087314 SCV001810604 likely benign Glycogen storage disease, type II 2021-07-22 criteria provided, single submitter clinical testing
Broad Institute Rare Disease Group, Broad Institute RCV001087314 SCV001422777 likely benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The c.1416C>T (p.Thr472=) 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 and a likely benign variant by Invitae and GeneDx in ClinVar (Variation ID: 456376). This variant has been identified in 0.008% (2/24284) of African chromosomes and 0.005% (6/127366) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs368492669). 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).
Natera, Inc. RCV001087314 SCV001453427 likely benign Glycogen storage disease, type II 2020-06-18 no assertion criteria provided clinical testing

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