ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.8580C>T (p.Ser2860=) (rs767368987)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000370881 SCV000474520 likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Invitae RCV000480585 SCV000562411 likely benign not provided 2016-12-20 criteria provided, single submitter clinical testing
GeneDx RCV000480585 SCV000570345 uncertain significance not provided 2016-05-15 criteria provided, single submitter clinical testing To our knowledge, the c.8580 C>T variant has not been published as a pathogenic variant nor has it been reported as a benign variant. It was not observed in approximately 6,400 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This nucleotide change occurs at a position that is conserved in mammals and results in a synonymous amino acid substitution. It is not predicted to affect splicing; however, the actual effect of the c.8580 C>T sequence change in vivo is unknown in the absence of RNA studies. Additionally, few pathogenic missense variants have been reported in CHARGE syndrome, as most pathogenic variants introduce a premature termination codon. Therefore, based on the currently available information, it is unclear whether c.8580 C>T, or S2860S, is a disease-causing or rare benign variant.
Invitae RCV001433530 SCV001636320 likely benign CHARGE association 2016-12-13 criteria provided, single submitter clinical testing

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