ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.1356C>T (p.Ala452=) (rs757893858)

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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 RCV000725823 SCV000339627 uncertain significance not provided 2016-02-16 criteria provided, single submitter clinical testing
GeneDx RCV000312644 SCV000717256 likely benign not specified 2017-12-11 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.
Blueprint Genetics RCV000725823 SCV000927550 uncertain significance not provided 2018-02-27 criteria provided, single submitter clinical testing
Invitae RCV001001227 SCV001043667 likely benign Glycogen storage disease, type II 2020-12-04 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001001227 SCV001158390 likely benign Glycogen storage disease, type II 2019-05-03 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001001227 SCV001282567 uncertain significance Glycogen storage disease, type II 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Broad Institute Rare Disease Group, Broad Institute RCV001001227 SCV001422896 likely benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The c.1356C>T (p.Ala452=) 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 Blueprint Genetics and likely benign by GeneDx in ClinVar (Variation ID: 286268). This variant has been identified in 0.014% (5/35404) of Latino chromosomes and 0.010% (13/128368) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs757893858). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. 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: PM2, BP4, BP7 (Richards 2015).
Natera, Inc. RCV001001227 SCV001453426 uncertain significance Glycogen storage disease, type II 2020-01-24 no assertion criteria provided clinical testing

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