ClinVar Miner

Submissions for variant NM_000258.3(MYL3):c.81T>C (p.Pro27=) (rs147584015)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000036034 SCV000059686 benign not specified 2012-07-06 criteria provided, single submitter clinical testing Pro27Pro in Exon 01 of MYL3: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue, is not located within t he splice consensus sequence and has been identified in 0.3% (13/3738) of Africa n American chromosomes from a broad population by the NHLBI Exome Sequencing Pro ject (http://evs.gs.washington.edu/EVS; dbSNP rs147584015).
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000036034 SCV000110308 likely benign not specified 2015-08-12 criteria provided, single submitter clinical testing
Invitae RCV000233955 SCV000284305 benign Hypertrophic cardiomyopathy 2020-12-03 criteria provided, single submitter clinical testing
Ambry Genetics RCV000241642 SCV000318425 likely benign Cardiovascular phenotype 2015-08-12 criteria provided, single submitter clinical testing Subpopulation frequency in support of benign classification;Synonymous alterations with insufficient evidence to classify as benign
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV000770183 SCV000901611 benign Cardiomyopathy 2016-10-12 criteria provided, single submitter clinical testing
Color Health, Inc RCV000770183 SCV000913787 benign Cardiomyopathy 2018-10-16 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000036034 SCV000919838 benign not specified 2018-11-19 criteria provided, single submitter clinical testing Variant summary: MYL3 c.81T>C 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 0.00045 in 276222 control chromosomes, predominantly within the African subpopulation at a frequency of 0.0048 in the gnomAD database. The observed variant frequency within African control individuals in the gnomAD database is approximately 190 fold of the estimated maximal expected allele frequency for a pathogenic variant in MYL3 causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.81T>C in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. Co-occurrences with other pathogenic variant(s) have been reported (TTR c.424G>A, p.Val142Ile), providing supporting evidence for a benign role. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and all these laboratories classified the variant as benign (1x) / likely benign (2x). Based on the evidence outlined above, the variant was classified as benign.
Illumina Clinical Services Laboratory,Illumina RCV001148456 SCV001309355 uncertain significance Familial hypertrophic cardiomyopathy 8 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, 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.
CeGaT Praxis fuer Humangenetik Tuebingen RCV001200161 SCV001371050 likely benign not provided 2020-04-01 criteria provided, single submitter clinical testing
GeneDx RCV001200161 SCV001940611 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Clinical Genetics,Academic Medical Center RCV000036034 SCV001917166 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV001200161 SCV001953966 likely benign not provided no assertion criteria provided clinical testing

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