ClinVar Miner

Submissions for variant NM_004006.3(DMD):c.3021G>A (p.Ser1007=) (rs1800268)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000080536 SCV000112438 benign not specified 2014-03-31 criteria provided, single submitter clinical testing
GeneDx RCV000080536 SCV000168174 benign not specified 2014-03-12 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.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000080536 SCV000268954 benign not specified 2014-10-29 criteria provided, single submitter clinical testing p.Ser1007Ser in exon 23 of DMD: This variant is not expected to have clinical si gnificance because it has been identified in 1.7% (112/6728) of European America n chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.ed u/EVS/; dbSNP rs1800268).
Invitae RCV000231618 SCV000288051 benign Duchenne muscular dystrophy 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000080536 SCV000309928 benign not specified criteria provided, single submitter clinical testing
Ambry Genetics RCV000241805 SCV000319072 benign Cardiovascular phenotype 2015-06-12 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000080536 SCV000603354 benign not specified 2018-07-05 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001167431 SCV001329931 benign Dilated cardiomyopathy 3B 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.
Integrated Genetics/Laboratory Corporation of America RCV000080536 SCV001361883 benign not specified 2019-02-18 criteria provided, single submitter clinical testing Variant summary: DMD c.3021G>A alters a non-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 0.012 in 204360 control chromosomes, predominantly within the Non-Finnish European subpopulation at a frequency of 0.02 in the gnomAD database, including 11 homozygotes and 717 hemizygotes. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 1.8 fold of the estimated maximal expected allele frequency for a pathogenic variant in DMD causing Duchenne muscular dystrophy phenotype (0.011), strongly suggesting that the variant is a benign polymorphism. To our knowledge, no occurrence of c.3021G>A in individuals affected with Duchenne muscular dystrophy and no experimental evidence demonstrating its impact on protein function have been reported. Three ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as benign. Based on the evidence outlined above, the variant was classified as benign.

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