ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.5824C>T (p.Arg1942Trp)

gnomAD frequency: 0.00003  dbSNP: rs200441929
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000634442 SCV000755749 benign CHARGE association 2023-12-30 criteria provided, single submitter clinical testing
Ambry Genetics RCV002317386 SCV000850732 uncertain significance Inborn genetic diseases 2018-08-26 criteria provided, single submitter clinical testing The p.R1942W variant (also known as c.5824C>T), located in coding exon 28 of the CHD7 gene, results from a C to T substitution at nucleotide position 5824. The arginine at codon 1942 is replaced by tryptophan, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on available evidence to date, the clinical significance of this variant remains unclear.
Eurofins Ntd Llc (ga) RCV000729031 SCV000856665 uncertain significance not provided 2017-09-14 criteria provided, single submitter clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV000634442 SCV002767727 uncertain significance CHARGE association 2020-05-25 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as a 3C-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from arginine to tryptophan, exon 29. (N) 0251 - Variant is heterozygous. (N) 0302 - Variant is present in gnomAD <0.001 for a dominant condition. Overall frequency: 0.003%, 8 Het, 0 Hom (subpopulation Ashkenazi Jewish: 0.02%, 2 Het). (P) 0309 - An alternative amino acid change at the same position has been observed in gnomAD: p.(Arg1942Gln) (0.0008%, 1 het). Note: other changes also seen in the surrounding arginine residues, a string of five arginine residues . (N) 0502 - Missense variant with conflicting in silico predictions and/or uninformative conservation. Only 1/4 in silico analyses damaging, glycine observed in sheep no changes in mammals and major amino acid change. (N) 0603 - Missense variant in a region that is highly intolerant to missense variation (high constraint region) (P) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0804 - Variant is absent in the population / or present in the population at <0.001 and has previously been described as variant of uncertain significance in multiple independent cases with consistent phenotype. ClinVar: 3x submitted as a VUS (1x Neurodevelopmental disorder, 1x CHARGE, 1x Not provided). (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign
Fulgent Genetics, Fulgent Genetics RCV002499049 SCV002814771 uncertain significance CHARGE association; Hypogonadotropic hypogonadism 5 with or without anosmia 2022-04-14 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000729031 SCV003917607 uncertain significance not provided 2023-02-01 criteria provided, single submitter clinical testing CHD7: PP3
Yale Center for Mendelian Genomics, Yale University RCV001849422 SCV002106784 uncertain significance Amenorrhea 2021-03-08 no assertion criteria provided literature only

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