ClinVar Miner

Submissions for variant NM_001271208.2(NEB):c.5102T>C (p.Val1701Ala) (rs117271684)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000117760 SCV000230591 benign not specified 2015-02-13 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000117760 SCV000307359 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001082597 SCV000416994 benign Nemaline myopathy 2 2018-01-12 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.
Invitae RCV001082597 SCV000640810 benign Nemaline myopathy 2 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586476 SCV000697833 benign not provided 2017-04-24 criteria provided, single submitter clinical testing Variant summary: The NEB c.5102T>C (p.Val1701Ala) variant involves the alteration of a conserved nucleotide and is predicted to be benign by 2/4 in silico tools (SNPs&GO not captured due to low reliability index). This variant was found in 962/107782 control chromosomes (24 homozygotes) from ExAC, predominantly observed in the East Asian subpopulation at a frequency of 0.081239 (640/7878). This frequency is about 23 times the estimated maximal expected allele frequency of a pathogenic NEB variant (0.0035355), suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Athena Diagnostics Inc RCV000586476 SCV000842874 benign not provided 2018-03-26 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000117760 SCV000152017 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.
GeneDx RCV000117760 SCV000519883 benign not specified 2016-05-18 no assertion criteria provided 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.

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