ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.2553G>A (p.Gly851=) (rs1042397)

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Total submissions: 12
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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 RCV000399277 SCV001371711 benign Glycogen storage disease, type II 2020-01-23 reviewed by expert panel curation The highest continental population minor allele frequency for c.2553G>A (p.Gly851=) in gnomAD v2.1.1 is 0.63818 in the European non-Finnish population. Note that the minor allele frequency is even higher in the Ashkenazi Jewish (0.70216) and European Finnish (0.64436) populations. These allele frequencies are higher than the ClinGen LSD VCEP's BA1 threshold (>0.01), meeting this criterion. There is a ClinVar entry for this variant (Variation ID: 92481, two star review status), with 6 submitters classifying the variant as 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 RCV000078176 SCV000110014 benign not specified 2018-09-04 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000078176 SCV000151257 benign not specified 2013-08-15 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000078176 SCV000302682 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000399277 SCV000407302 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.
Invitae RCV000399277 SCV001725524 benign Glycogen storage disease, type II 2020-12-04 criteria provided, single submitter clinical testing
Nilou-Genome Lab RCV000399277 SCV001737958 benign Glycogen storage disease, type II 2021-06-10 criteria provided, single submitter clinical testing
GeneDx RCV000675248 SCV001888124 benign not provided 2015-03-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 23418865)
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000399277 SCV000733737 benign Glycogen storage disease, type II no assertion criteria provided clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000675248 SCV000800895 benign not provided 2015-10-19 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000675248 SCV001551765 uncertain significance not provided no assertion criteria provided clinical testing multiple AR variants in same gene - keep for nowAllele frequency is common in at least one population database (frequency: 70.344% in gnomAD_ExomesFounderPop) based on the frequency threshold of 2.76% for this gene.Variant was observed in a homozygous state in population databases more than expected for disease.6 reputable source/s reports the variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.A synonymous variant not located in a splice region.
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000078176 SCV001930236 benign not specified no assertion criteria provided clinical testing

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