ClinVar Miner

Submissions for variant NM_004006.3(DMD):c.3734C>T (p.Thr1245Ile) (rs1800269)

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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 RCV000080593 SCV000112495 benign not specified 2015-08-10 criteria provided, single submitter clinical testing
GeneDx RCV000080593 SCV000168178 benign not specified 2013-10-14 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 RCV000080593 SCV000268957 benign not specified 2015-01-13 criteria provided, single submitter clinical testing p.Thr1245Ile in exon 27 of DMD: This variant is not expected to have clinical si gnificance because it has been identified in 1.1% (73/6728) of European American chromosomes by the NHLBI Exome Sequencing Project ( /EVS/; dbSNP rs1800269).
PreventionGenetics,PreventionGenetics RCV000080593 SCV000309931 benign not specified criteria provided, single submitter clinical testing
Ambry Genetics RCV000252057 SCV000318573 benign Cardiovascular phenotype 2015-06-19 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 RCV000345231 SCV000482260 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.
Invitae RCV000475998 SCV000560862 benign Duchenne muscular dystrophy 2019-12-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000080593 SCV000885290 benign not specified 2018-08-15 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000080593 SCV001339232 benign not specified 2020-03-12 criteria provided, single submitter clinical testing Variant summary: DMD c.3734C>T (p.Thr1245Ile) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.019 in 182401 control chromosomes, predominantly at a frequency of 0.089 within the Latino subpopulation in the gnomAD database, including 112 homozygotes and 971 hemizygotes. The observed variant frequency within Latino control individuals in the gnomAD database is significantly higher than expected for a pathogenic variant in DMD causing Dystrophinopathies phenotype, strongly suggesting that the variant is a benign polymorphism found primarily in populations of Latino origin. Six ClinVar submitters (evaluation after 2014) cite the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.

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