ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.1438-9G>A

gnomAD frequency: 0.00056  dbSNP: rs202211401
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001087242 SCV000626514 likely benign Glycogen storage disease, type II 2024-01-27 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000727404 SCV000708267 uncertain significance not provided 2017-05-02 criteria provided, single submitter clinical testing
GeneDx RCV000594051 SCV000715508 likely benign not specified 2017-09-06 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.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard RCV001087242 SCV001422888 likely benign Glycogen storage disease, type II 2020-01-22 criteria provided, single submitter curation The c.1438-9G>A 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: 456379). This variant has been identified in 0.213% (53/24882) of African chromosomes and 0.035% (7/19946) of East Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs202211401). 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 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: BP4, BP7 (Richards 2015).
PreventionGenetics, part of Exact Sciences RCV003942733 SCV004761518 likely benign GAA-related condition 2020-11-18 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV001087242 SCV001455616 likely benign Glycogen storage disease, type II 2020-09-16 no assertion criteria provided clinical testing

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