ClinVar Miner

Submissions for variant NM_182914.3(SYNE2):c.16718G>A (p.Arg5573Gln)

gnomAD frequency: 0.00091  dbSNP: rs149227847
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000180739 SCV000233224 uncertain significance not provided 2015-05-27 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000526342 SCV000387565 benign Emery-Dreifuss muscular dystrophy 5, autosomal dominant 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV000526342 SCV000648881 likely benign Emery-Dreifuss muscular dystrophy 5, autosomal dominant 2023-12-11 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002469047 SCV002766554 likely benign not specified 2022-11-29 criteria provided, single submitter clinical testing Variant summary: SYNE2 c.16718G>A (p.Arg5573Gln) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00082 in 251384 control chromosomes, predominantly at a frequency of 0.0019 within the Latino subpopulation in the gnomAD database, suggesting that it is a benign polymorphism found primarily in individuals of Latino ancestry. To our knowledge, no occurrence of c.16718G>A in individuals affected with Autosomal Dominant Emery-Dreifuss Muscular Dystrophy 5 and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as benign, one as likely benign, and one classified it as VUS. Based on the evidence outlined above, the variant was classified as likely benign.
CeGaT Center for Human Genetics Tuebingen RCV000180739 SCV004134278 benign not provided 2023-06-01 criteria provided, single submitter clinical testing SYNE2: BP4, BS1, BS2
PreventionGenetics, part of Exact Sciences RCV003955103 SCV004773720 likely benign SYNE2-related disorder 2022-12-01 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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