ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.277A>G (p.Thr93Ala) (rs398124317)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000081825 SCV000113760 uncertain significance not provided 2015-09-02 criteria provided, single submitter clinical testing
Invitae RCV000796849 SCV000936379 uncertain significance CHARGE association 2019-11-25 criteria provided, single submitter clinical testing This sequence change replaces threonine with alanine at codon 93 of the CHD7 protein (p.Thr93Ala). The threonine residue is weakly conserved and there is a small physicochemical difference between threonine and alanine. This variant is present in population databases (rs398124317, ExAC 0.04%), and has an allele count higher than expected for a pathogenic variant (PMID: 28166811). This variant has been observed in an individual affected with atrioventricular septal defect (PMID: 25996639). ClinVar contains an entry for this variant (Variation ID: 95780). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The alanine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
GeneDx RCV000081825 SCV000980456 likely benign not provided 2018-04-24 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.

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