ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2446G>A (p.Val816Ile) (rs1800314)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel, ClinGen RCV000296830 SCV001371702 benign Glycogen storage disease, type II 2020-01-23 reviewed by expert panel curation The highest continental population minor allele frequency for c.2446G>A (p.Val816Ile) in gnomAD v2.1.1 is 0.14249 in the African population. This is higher than the ClinGen LSD VCEP's BA1 threshold (>0.01), therefore meeting the BA1 criterion. There is a ClinVar entry for this variant (Variation ID: 92477; 2 star review status) with four submitters classifying the variant as benign, and two as likely benign. In summary, this variant meets the criteria to be classified as benign for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: BA1.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000078172 SCV000110010 benign not specified 2013-08-13 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000078172 SCV000302680 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000296830 SCV000407300 benign Glycogen storage disease, type II 2018-01-12 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Phosphorus, Inc. RCV000296830 SCV000679767 benign Glycogen storage disease, type II 2017-08-01 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000078172 SCV000151256 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000675246 SCV000800893 benign not provided 2017-05-17 no assertion criteria provided clinical testing

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