ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.915G>A (p.Gly305=) (rs150343359)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000723389 SCV000330943 uncertain significance not provided 2018-08-10 criteria provided, single submitter clinical testing
GeneDx RCV000168660 SCV000525438 likely benign not specified 2017-07-14 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.
Invitae RCV001079201 SCV000626654 likely benign Glycogen storage disease, type II 2020-12-07 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001079201 SCV001285461 uncertain significance Glycogen storage disease, type II 2018-01-13 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001079201 SCV001473234 likely benign Glycogen storage disease, type II 2019-12-09 criteria provided, single submitter clinical testing
Nilou-Genome Lab RCV001079201 SCV001712370 likely benign Glycogen storage disease, type II 2021-05-18 criteria provided, single submitter clinical testing
Broad Institute Rare Disease Group, Broad Institute RCV001079201 SCV001423082 likely benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The c.915G>A (p.Gly305=) variant in GAA has been reported in 2 individuals with limb-girdle muscle weakness (PMID: 29149851) and has also been reported as a likely benign variant by GeneDx and Invitae and as a VUS by EGL in ClinVar (Variation ID: 188478). This variant has been identified in 0.1843% (232/125858) of European (non-Finnish) chromosomes and 0.1138% (40/35140) of Latino chromosomes by the Genome Aggregation Database (gnomAD,; dbSNP rs150343359). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Computational prediction tools (including splice predictors) and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. 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: BP4, BP7 (Richards 2015).
Natera, Inc. RCV001079201 SCV001453420 likely benign Glycogen storage disease, type II 2020-01-10 no assertion criteria provided clinical testing

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