ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.5440G>A (p.Ala1814Thr) (rs368609862)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000337409 SCV000474454 uncertain significance CHARGE association 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000390634 SCV000474455 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.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000825306 SCV000966601 uncertain significance not specified 2018-03-29 criteria provided, single submitter clinical testing Variant classified as Uncertain Significance - Favor Benign. The p.Ala1814Thr va riant in CHD7 has been reported in 1 individual with a sex development disorder (Eggers 2016), but has not been reported in individuals with hearing loss or CHA RGE syndrome. This variant has also been reported in Clin Var (Variation ID# 363 467). It has also been identified in 18/276340 total chromosomes by the Genome A ggregation Database (nomad, http://gnomad.broadinstitute.org/; dbSNP rs368609862 ). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Computational prediction tools and conservation analysis suggest that the p.Ala1814Thr variant may not impact the protein, though this information is not predictive enough to rule out pathog enicity. In summary, while the clinical significance of the p.Ala1814Thr variant is uncertain, these data suggest that it is more likely to be benign. ACMG/AMP Criteria applied: BP4.

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