ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.1179A>G (p.Pro393=) (rs111238892)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000242796 SCV000312944 benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000242796 SCV000332531 benign not specified 2015-07-08 criteria provided, single submitter clinical testing
Invitae RCV001084585 SCV000631237 benign CHARGE association 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588342 SCV000699431 benign not provided 2016-06-27 criteria provided, single submitter clinical testing Variant summary: The CHD7 c.1179A>G (p.Pro393Pro) 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. 4/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 50/120332 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0047959 (47/9800). This frequency is about 110 times the estimated maximal expected allele frequency of a pathogenic CHD7 variant (0.0000438), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. This variant has been reported as a benign variant in one CHARGE syndrome patient (Janssen_HM_2012). Taken together, this variant is classified as benign.
Ambry Genetics RCV000717088 SCV000847934 likely benign History of neurodevelopmental disorder 2016-10-03 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign;In silico models in agreement (benign)
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000242796 SCV000967053 benign not specified 2017-08-23 criteria provided, single submitter clinical testing p.Pro393Pro in exon 2 of CHD7: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 0.48% (47/9800) of Af rican chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadin stitute.org; dbSNP rs111238892).

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