ClinVar Miner

Submissions for variant NM_001271.4(CHD2):c.4984C>T (p.His1662Tyr)

gnomAD frequency: 0.00007  dbSNP: rs146275216
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001697925 SCV000725403 likely benign not provided 2021-03-25 criteria provided, single submitter clinical testing
Invitae RCV000651634 SCV000773488 uncertain significance Developmental and epileptic encephalopathy 94 2024-01-24 criteria provided, single submitter clinical testing This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 1662 of the CHD2 protein (p.His1662Tyr). This variant is present in population databases (rs146275216, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with CHD2-related conditions. ClinVar contains an entry for this variant (Variation ID: 513867). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CHD2 protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002531601 SCV003661248 likely benign Inborn genetic diseases 2022-12-28 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.
Revvity Omics, Revvity RCV000651634 SCV004237811 likely benign Developmental and epileptic encephalopathy 94 2019-11-20 criteria provided, single submitter clinical testing
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille RCV001252448 SCV001428204 likely benign Intellectual disability 2019-01-01 no assertion criteria provided clinical testing

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