ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.547-39T>G (rs12452721)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000246553 SCV000302689 benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000246553 SCV000856219 benign not specified 2017-08-07 criteria provided, single submitter clinical testing
Invitae RCV001249010 SCV001725516 benign Glycogen storage disease, type II 2020-12-04 criteria provided, single submitter clinical testing
Nilou-Genome Lab RCV001249010 SCV001738008 benign Glycogen storage disease, type II 2021-06-10 criteria provided, single submitter clinical testing
Broad Institute Rare Disease Group, Broad Institute RCV001249010 SCV001422857 benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The c.547-39T>G variant in GAA has been reported in at least 6 individuals with suspected glycogen storage disease II (PMID: 28032299, 25681614), and has also been reported in ClinVar (VariationID: 255363) as benign by EGL Genetic Diagnostics and PreventionGenetics. This variant has been identified in 77.9% (8028/10312) of Ashkenazi Jewish chromosomes, including 3120 homozygotes, and is present at high frequencies in other populations, by the Genome Aggregation Database (gnomAD,; dbSNP rs12452721). This variant has been seen in the general population at a frequency 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, this variant meets criteria to be classified as benign for glycogen storage disease II in an autosomal recessive manner based on high frequency in the general population. ACMG/AMP Criteria applied: BA1, BP7, BP4 (Richards 2015).

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