ClinVar Miner

Submissions for variant NM_000642.3(AGL):c.2802A>C (p.Ala934=) (rs34230588)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000245574 SCV000305385 benign not specified criteria provided, single submitter clinical testing
Invitae RCV001083631 SCV000626708 benign Glycogen storage disease type III 2020-12-07 criteria provided, single submitter clinical testing
GeneDx RCV000245574 SCV000731011 benign not specified 2017-04-04 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000245574 SCV000918402 benign not specified 2018-03-29 criteria provided, single submitter clinical testing Variant summary: AGL c.2802A>C alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0023 in 276798 control chromosomes, predominantly within the African subpopulation at a frequency of 0.025, including 3 homozygotes (gnomAD). The observed variant frequency within African control individuals in the gnomAD database is approximately 11-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in AGL causing Glycogen Storage Disease Type III phenotype (0.0023), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.2802A>C in individuals affected with Glycogen Storage Disease Type III and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as "benign." Based on the evidence outlined above, the variant was classified as benign.
Mayo Clinic Laboratories, Mayo Clinic RCV000675331 SCV000800997 likely benign not provided 2017-10-16 no assertion criteria provided clinical testing
Natera, Inc. RCV001083631 SCV001456536 benign Glycogen storage disease type III 2020-09-16 no assertion criteria provided clinical testing

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