ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.309G>A (p.Ser103=) (rs115293759)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000081829 SCV000113764 benign not specified 2013-09-26 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000081829 SCV000312968 likely benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000081829 SCV000512577 benign not specified 2016-04-22 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 RCV001081291 SCV000562417 benign CHARGE association 2020-12-02 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586712 SCV000699436 benign not provided 2016-06-27 criteria provided, single submitter clinical testing Variant summary: The CHD7 c.309G>A (p.Ser103Ser) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant, but 5/5 splicing algorithms predict no significant change to normal splicing. This variant was found in 199/119626 control chromosomes (3 homozygotes) at a frequency of 0.0016635, which is approximately 1331 times the estimated maximal expected allele frequency of a pathogenic CHD7 variant (0.0000013), suggesting this variant is likely a benign polymorphism. The variant has been cited in at least one CHARGE syndrome patient in the literature without evidence of causality (Jain_Int J Pediatr Endocrinol_2011). In addition, one clinical diagnostic laboratory classified this variant as benign. Based on the synonymous nature of this variant and the high allele frequency in the general population, this variant was classified as benign.
Ambry Genetics RCV000716504 SCV000847345 benign History of neurodevelopmental disorder 2016-07-01 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000081829 SCV001365640 benign not specified 2017-08-23 criteria provided, single submitter clinical testing p.Ser103Ser in exon 2 of CHD7: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 1.89% (183/9668) of African chromosomes by the Exome Aggregation Consortium (ExAC,; dbSNP rs115293759).

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