ClinVar Miner

Submissions for variant NM_001271208.2(NEB):c.9467T>A (p.Ile3156Asn) (rs145770770)

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Total submissions: 8
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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 RCV000224006 SCV000281035 benign not provided 2015-12-21 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000242273 SCV000307408 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000242273 SCV000519843 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.
Athena Diagnostics Inc RCV000242273 SCV000614186 likely benign not specified 2017-05-23 criteria provided, single submitter clinical testing
Invitae RCV000557476 SCV000640898 benign Nemaline myopathy 2 2020-12-08 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000242273 SCV001361229 benign not specified 2019-04-22 criteria provided, single submitter clinical testing Variant summary: NEB c.9467T>A (p.Ile3156Asn) results in a non-conservative amino acid change in the encoded protein sequence. One of two in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.011 in 280432 control chromosomes, predominantly at a frequency of 0.021 within the South Asian subpopulation in the gnomAD database, including 8 homozygotes. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 6-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 a benign polymorphism found primarily in populations of South Asian origin. To our knowledge, no occurrence of c.9467T>A in individuals affected with Nemaline Myopathy 2 and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely benign/benign. Based on the evidence outlined above, the variant was classified as benign.
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000224006 SCV001800344 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000242273 SCV001929890 benign not specified no assertion criteria provided clinical testing

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