ClinVar Miner

Submissions for variant NM_000337.5(SGCD):c.213G>A (p.Arg71=) (rs74846539)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000041402 SCV000065097 likely benign not specified 2015-05-18 criteria provided, single submitter clinical testing p.Arg71Arg in exon 4 of SGCD: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 0.15% (95/64128) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broa dinstitute.org; dbSNP rs74846539).
Invitae RCV001083678 SCV000262239 likely benign Autosomal recessive limb-girdle muscular dystrophy type 2F 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000041402 SCV000303682 likely benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000725174 SCV000334630 uncertain significance not provided 2015-08-25 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000334932 SCV000455476 uncertain significance Qualitative or quantitative defects of delta-sarcoglycan 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Clinical Services Laboratory,Illumina RCV000299902 SCV000455478 likely benign Limb-Girdle Muscular Dystrophy, Recessive 2016-06-14 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV000770205 SCV000901634 benign Cardiomyopathy 2019-03-04 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000725174 SCV001154568 likely benign not provided 2017-03-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000041402 SCV001159577 likely benign not specified 2019-05-03 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000041402 SCV001363520 benign not specified 2019-05-28 criteria provided, single submitter clinical testing Variant summary: SGCD c.213G>A alters a 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 0.0012 in 248064 control chromosomes in the gnomAD database, including 2 homozygotes. The observed variant frequency is approximately 48 fold of the estimated maximal expected allele frequency for a pathogenic variant in SGCD causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.213G>A in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, four of whom classified the variant as likely benign and one as a VUS. Based on the evidence outlined above, the variant was classified as benign.

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