ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2415G>A (p.Val805=) (rs150536507)

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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 RCV000724845 SCV000226557 uncertain significance not provided 2018-04-13 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000390395 SCV000407299 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.
GeneDx RCV000175125 SCV000524470 likely benign not specified 2017-12-21 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 RCV000390395 SCV000626568 likely benign Glycogen storage disease, type II 2020-12-02 criteria provided, single submitter clinical testing
Broad Institute Rare Disease Group, Broad Institute RCV000390395 SCV001422812 likely benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The heterozygous c.2415G>A (p.Val805=) variant in GAA has been reported as a likely benign variant (by GeneDx and Invitae) and a VUS (by EGL Genetic Diagnostics and Illumina) for Glycogen Storage Disease II in ClinVar (Variation ID: 194697). This variant has been identified in 0.1495% (189/126462) of European (non-Finnish) chromosomes and 0.1387% (49/35320) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs150536507). 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. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely benign. ACMG/AMP Criteria applied: BP7, BP4 (Richards 2015).
Natera, Inc. RCV000390395 SCV001455440 uncertain significance Glycogen storage disease, type II 2019-11-11 no assertion criteria provided clinical testing

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