ClinVar Miner

Submissions for variant NM_000426.4(LAMA2):c.7431A>T (p.Arg2477Ser)

gnomAD frequency: 0.00914  dbSNP: rs34367843
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000224349 SCV000281508 likely benign not provided 2016-04-28 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
PreventionGenetics,PreventionGenetics RCV000117449 SCV000304180 benign not specified criteria provided, single submitter clinical testing
Eurofins NTD LLC (GA) RCV000117449 SCV000331864 benign not specified 2016-03-01 criteria provided, single submitter clinical testing
GeneDx RCV000117449 SCV000513435 benign not specified 2016-08-05 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.
Athena Diagnostics Inc RCV000117449 SCV000613982 benign not specified 2016-10-28 criteria provided, single submitter clinical testing
Invitae RCV001086841 SCV000658762 benign LAMA2-related muscular dystrophy 2021-12-18 criteria provided, single submitter clinical testing
Mendelics RCV000987777 SCV001137228 benign Merosin deficient congenital muscular dystrophy 2019-05-28 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV001155022 SCV001316422 likely benign Congenital muscular dystrophy due to partial LAMA2 deficiency 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000117449 SCV002500203 benign not specified 2022-03-08 criteria provided, single submitter clinical testing Variant summary: LAMA2 c.7431A>T (p.Arg2477Ser) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0022 in 250318 control chromosomes, predominantly at a frequency of 0.029 within the African or African-American subpopulation in the gnomAD database, including 9 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 12.97 fold of the estimated maximal expected allele frequency for a pathogenic variant in LAMA2 causing Laminin Alpha 2-Related Dystrophy phenotype (0.0022), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. 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.
Genetic Services Laboratory,University of Chicago RCV000117449 SCV000151663 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

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