ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.657C>T (p.Gly219=) (rs113483301)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000081851 SCV000113786 benign not specified 2014-10-28 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000145687 SCV000192793 uncertain significance CHARGE association 2013-02-08 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000081851 SCV000312993 likely benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000395599 SCV000474375 benign Hypogonadotropic hypogonadism 5 with or without anosmia 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.
Invitae RCV000145687 SCV000562425 benign CHARGE association 2020-12-02 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590132 SCV000699438 benign not provided 2016-06-27 criteria provided, single submitter clinical testing Variant summary: The CHD7 c.657C>T (p.Gly219Gly) variant involves the alteration of a conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant and 4/5 slice site tools predict the variant not to have an impact on normal splicing. This variant was found in 285/120590 control chromosomes (9 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.027295 (267/9782). This frequency is about 21836 times the estimated maximal expected allele frequency of a pathogenic CHD7 variant (0.0000013), highly suggesting this is a benign polymorphism found primarily in the populations of African origin. The variant was identified in at least one African American atypical CHARGE syndrome case reported in the literature without providing evidence of causality (ie. functional studies on the variant or co-segregation with disease). A clinical diagnostic laboratory and a publication classify the variant as benign (Bartels_GTMB_2010). Taken together and based on the synonymous nature of the variant and its high allele frequency in the general population, this variant was classified as Benign.
Ambry Genetics RCV000716490 SCV000847331 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 RCV000081851 SCV000967052 benign not specified 2017-08-23 criteria provided, single submitter clinical testing p.Gly219Gly 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 2.73% (267/9782) of A frican chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadi nstitute.org; dbSNP rs113483301).
GeneDx RCV000590132 SCV001900547 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000081851 SCV000192820 likely benign not specified no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000081851 SCV001920946 benign not specified no assertion criteria provided clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000081851 SCV001957886 benign not specified no assertion criteria provided clinical testing

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