ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2668G>C (p.Val890Leu) (rs377286472)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000245954 SCV000302683 benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000245954 SCV000334977 benign not specified 2015-09-18 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000305205 SCV000407303 likely benign Glycogen storage disease, type II 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000245954 SCV000524863 benign not specified 2016-08-08 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 RCV000305205 SCV000626591 benign Glycogen storage disease, type II 2019-12-31 criteria provided, single submitter clinical testing
Center for Advanced Laboratory Medicine, UC San Diego Health,University of California San Diego RCV000852734 SCV000995449 likely benign Hypertrophic cardiomyopathy 2017-11-14 criteria provided, single submitter clinical testing
Broad Institute Rare Disease Group,Broad Institute RCV000305205 SCV001422936 benign Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The p.Val890Leu variant in GAA has been reported as a benign variant (by GeneDx, Invitae, EGL, and Prevention Genetics) and a VUS (by Illumina) in ClinVar (Variation ID: 255361). This variant has been identified in 2.652% (812/30616) of South Asian chromosomes, including 13 homozygotes, as well as other populations at lesser frequencies by the Genome Aggregation Database (gnomAD,; dbSNP rs377286472). This variant has been seen in the general population at a frequency 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. In summary, this variant meets criteria to be classified as benign for Glycogen Storage Disease II in an autosomal recessive manner based on its frequency in the general population. ACMG/AMP Criteria applied: BA1, BP4 (Richards 2015).

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