ClinVar Miner

Submissions for variant NM_000742.4(CHRNA2):c.1434C>A (p.Asp478Glu)

gnomAD frequency: 0.00307  dbSNP: rs56344740
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000124278 SCV000167705 benign not specified 2013-05-13 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 RCV001080927 SCV000285613 benign Autosomal dominant nocturnal frontal lobe epilepsy 2024-01-27 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000768183 SCV000473182 benign Autosomal dominant nocturnal frontal lobe epilepsy 4 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.
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000419685 SCV000511714 likely benign not provided 2016-09-01 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Eurofins Ntd Llc (ga) RCV000124278 SCV000706592 likely benign not specified 2017-03-13 criteria provided, single submitter clinical testing
Ambry Genetics RCV002312821 SCV000848373 likely benign Inborn genetic diseases 2018-09-09 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768183 SCV000898604 uncertain significance Autosomal dominant nocturnal frontal lobe epilepsy 4 2021-03-30 criteria provided, single submitter clinical testing CHRNA2 NM_000742 exon 6 p.Asp478Glu (c.1434C>A): This variant has not been reported in the literature but is present in 0.5% (685/126322) of European alleles, including 1 homozygote, in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs56344740). This variant is present in ClinVar, with several labs classifying this variant as likely benign or benign (Variation ID:136753). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. Functional studies predict that this variant will impact the protein (Dash 2014 PMID:24950454). However, these studies may not accurately represent human biological function. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Athena Diagnostics Inc RCV000419685 SCV001143532 benign not provided 2018-11-12 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV000768183 SCV001440254 likely benign Autosomal dominant nocturnal frontal lobe epilepsy 4 2019-01-01 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000419685 SCV004164534 benign not provided 2023-11-01 criteria provided, single submitter clinical testing CHRNA2: BS1, BS2

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