ClinVar Miner

Submissions for variant NM_004006.3(DMD):c.4162T>G (p.Phe1388Val) (rs28715870)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000080604 SCV000112506 benign not specified 2016-01-25 criteria provided, single submitter clinical testing
GeneDx RCV000080604 SCV000168180 benign not specified 2014-01-09 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 RCV000080604 SCV000268958 benign not specified 2015-01-13 criteria provided, single submitter clinical testing p.Phe1388Val in exon 30 of DMD: This variant is not expected to have clinical si gnificance because it has been identified in 9% (345/3833) of African American c hromosomes by the NHLBI Exome Sequencing Project ( VS/; dbSNP rs28715870).
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224025 SCV000281058 benign not provided 2015-06-04 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000080604 SCV000309932 benign not specified criteria provided, single submitter clinical testing
Ambry Genetics RCV000252226 SCV000318387 benign Cardiovascular phenotype 2016-02-15 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
Illumina Clinical Services Laboratory,Illumina RCV000375597 SCV000482255 benign Dilated cardiomyopathy 3B 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 RCV001084439 SCV000560845 benign Duchenne muscular dystrophy 2019-12-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000080604 SCV000883722 benign not specified 2018-10-23 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000080604 SCV001339233 benign not specified 2020-03-30 criteria provided, single submitter clinical testing Variant summary: DMD c.4162T>G (p.Phe1388Val) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0077 in 182914 control chromosomes in the gnomAD database, including 33 homozygotes and 364 hemizygotes. The observed variant frequency is approximately 695 fold of the estimated maximal expected allele frequency for a pathogenic variant in DMD causing Dystrophinopathies phenotype (1.1e-05), strongly suggesting that the variant is benign. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

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