ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.2436A>T (p.Lys812Asn) (rs61978638)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000417558 SCV000231753 uncertain significance not provided 2014-05-08 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000192622 SCV000247017 likely benign not specified 2015-06-30 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000417558 SCV000511030 likely benign not provided 2017-01-12 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000417558 SCV000699433 likely benign not provided 2017-03-27 criteria provided, single submitter clinical testing Variant summary: The CHD7 c.2436A>T (p.Lys812Asn) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 15/29850 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.004964 (15/3022). This frequency is about 113 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 in one CHARGE syndrome patient without strong evidence for causality (Janssen_HM_2012), and it has been classified as benign by multiple publications (Bergman_HM_2012, Janssen_HM_2012). In addition, multiple clinical diagnostic laboratories classified this variant as likely benign and one lab classified it as uncertain significance. Taken together, this variant is classified as likely benign.
Invitae RCV001083402 SCV000755755 benign CHARGE association 2020-11-20 criteria provided, single submitter clinical testing
Ambry Genetics RCV000719377 SCV000850243 likely benign History of neurodevelopmental disorder 2016-10-03 criteria provided, single submitter clinical testing In silico models in agreement (benign);Insufficient evidence;Subpopulation frequency in support of benign classification
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768180 SCV000898600 uncertain significance CHARGE association; Hypogonadotropic hypogonadism 5 with or without anosmia 2018-01-31 criteria provided, single submitter clinical testing CHD7 NM_017780 exon 6 p.Lys812Asn (c.2436A>T):This variant has not been reported in the literature but is present in 0.3% (59/19166) of African alleles in the Genome Aggregation Database ( This variant is present in ClinVar (Variation ID:198223). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000192622 SCV000966399 likely benign not specified 2018-08-09 criteria provided, single submitter clinical testing The p.Lys812Asn variant in CHD7 is classified as likely benign because it has be en identified in 0.3% (59/19166) of African chromosomes by the Genome Aggregatio n Database (gnomAD, ACMG/AMP Criteria applie d: BS1.
Illumina Clinical Services Laboratory,Illumina RCV001159419 SCV001321133 benign Hypogonadotropic hypogonadism 5 with or without anosmia 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
GeneDx RCV000417558 SCV001857082 benign not provided 2019-09-24 criteria provided, single submitter clinical testing
Human Genetics - Radboudumc,Radboudumc RCV000192622 SCV001958785 benign not specified no assertion criteria provided clinical testing

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