ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2481+16G>A (rs41292408)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000675247 SCV000110011 uncertain significance not provided 2016-08-30 criteria provided, single submitter clinical testing
GeneDx RCV000078173 SCV000519706 likely benign not specified 2017-06-13 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 RCV001249017 SCV001717000 benign Glycogen storage disease, type II 2020-11-21 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000675247 SCV000800894 likely benign not provided 2017-05-16 no assertion criteria provided clinical testing
Broad Institute Rare Disease Group, Broad Institute RCV001249017 SCV001422874 likely benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The c.2481+16G>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 GeneDx and Mayo Clinic Genetic Testing Laboratories in ClinVar (Variation ID: 92478). This variant has been identified in 0.367% (413/112458) of European (non-Finnish) chromosomes, including 2 homozygotes, and 0.328% (106/32290) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs41292408). 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).

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