ClinVar Miner

Submissions for variant NM_001271208.2(NEB):c.10338T>C (p.Asn3446=) (rs147569843)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000247721 SCV000307183 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000247721 SCV000528497 benign not specified 2016-07-08 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 RCV000586906 SCV000614159 benign not provided 2019-06-27 criteria provided, single submitter clinical testing
Invitae RCV001082593 SCV000640476 benign Nemaline myopathy 2 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586906 SCV000697796 benign not provided 2017-04-24 criteria provided, single submitter clinical testing Variant summary: The NEB c.10338T>C (p.Asn3446Asn) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts the creation of SRp40 binding site. However, these predictions have yet to be confirmed by functional studies. This variant was found in 926/120706 control chromosomes (19 homozygotes) from ExAC at a frequency of 0.0076715, which is approximately 2 times the estimated maximal expected allele frequency of a pathogenic NEB variant (0.0035355), suggesting this variant is likely a benign polymorphism. The variant is more common in East Asian population with allele frequency of 5.4% (465/8592 chromosomes). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Illumina Clinical Services Laboratory,Illumina RCV001082593 SCV001294685 benign Nemaline myopathy 2 2018-04-20 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.

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