ClinVar Miner

Submissions for variant NM_001164508.2(NEB):c.20766C>T (p.Asp6922=)

gnomAD frequency: 0.01163  dbSNP: rs34555492
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000117738 SCV000307291 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000525209 SCV000416857 benign Nemaline myopathy 2 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.
GeneDx RCV000117738 SCV000519548 benign not specified 2016-03-03 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.
Invitae RCV000525209 SCV000640672 benign Nemaline myopathy 2 2021-12-18 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000117738 SCV001361227 benign not specified 2019-04-22 criteria provided, single submitter clinical testing Variant summary: NEB c.20766C>T 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 0.015 in 280110 control chromosomes in the gnomAD database, including 68 homozygotes. The observed variant frequency is approximately 4-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in NEB causing Nemaline Myopathy 2 phenotype (0.0035), strongly suggesting that the variant is benign. Three ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant twice as benign and once as uncertain significance. Based on the evidence outlined above, the variant was classified as benign.
Genome-Nilou Lab RCV000525209 SCV001716393 benign Nemaline myopathy 2 2021-05-18 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001542860 SCV001761253 benign Arthrogryposis multiplex congenita 6 2021-07-10 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000117738 SCV000151989 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.
Natera, Inc. RCV000525209 SCV001463302 benign Nemaline myopathy 2 2020-09-16 no assertion criteria provided clinical testing

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