ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2253C>T (p.Leu751=)

gnomAD frequency: 0.00020  dbSNP: rs140441758
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000403504 SCV000345594 uncertain significance not provided 2018-02-07 criteria provided, single submitter clinical testing
Invitae RCV001080332 SCV000626556 likely benign Glycogen storage disease, type II 2024-01-21 criteria provided, single submitter clinical testing
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV001080332 SCV001422780 likely benign Glycogen storage disease, type II 2020-01-22 criteria provided, single submitter curation The c.2253C>T (p.Leu751=) 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 in ClinVar (Variation ID: 290924). This variant has been identified in 0.024% (6/24918) of African chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs140441758). 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).
Genome-Nilou Lab RCV001080332 SCV001810184 likely benign Glycogen storage disease, type II 2021-07-22 criteria provided, single submitter clinical testing
Ambry Genetics RCV002446535 SCV002736489 likely benign Cardiovascular phenotype 2022-03-04 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Natera, Inc. RCV001080332 SCV002092119 likely benign Glycogen storage disease, type II 2021-02-24 no assertion criteria provided clinical testing

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