ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.2990del (p.Leu997fs)

dbSNP: rs1554597677
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV000626339 SCV002768846 pathogenic CHARGE association 2021-05-06 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with CHARGE syndrome (MIM#214800) and hypogonadotropic hypogonadism 5 with or without anosmia (MIM#612370). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Frameshift and nonsense variants predicted to result in NMD are frequently reported as pathogenic in affected individuals (ClinVar, PMID:22461308). (SP) 0803 - This variant has limited previous evidence of pathogenicity in an unrelated individuals. An infant with clinically-diagnosed CHARGE syndrome and hypoglycaemia was reported in the literature with this variant (PMID:29355723). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1102 - Strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Fukami Lab, Dept of Molecular Endocrinology, National Research Institute for Child Health and Development RCV000626339 SCV000606861 pathogenic CHARGE association 2017-10-03 no assertion criteria provided clinical testing

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