ClinVar Miner

Submissions for variant NM_000233.4(LHCGR):c.458+3A>G (rs76210637)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Integrated Genetics/Laboratory Corporation of America RCV000030142 SCV000052797 likely benign Gonadotropin-independent familial sexual precocity 2011-08-18 criteria provided, single submitter curation Converted during submission to Likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000324216 SCV000431059 likely benign Leydig cell hypoplasia, type 1 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000030142 SCV000431060 benign Gonadotropin-independent familial sexual precocity 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Illumina Clinical Services Laboratory,Illumina RCV000283986 SCV000431061 likely benign Hypergonadotropic hypogonadism 2016-06-14 criteria provided, single submitter clinical testing
GeneDx RCV000522874 SCV000620635 uncertain significance not provided 2017-09-12 criteria provided, single submitter clinical testing The c.458+3 A>G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.458+3 A>G variant is observed in 237/66698 (0.36%) alleles, including one homozygote, from individuals of European background in the ExAC dataset (Lek et al., 2016). Several in-silico splice prediction models predict that c.458+3 A>G damages or destroys the natural splice donor site which may lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV000522874 SCV001110407 benign not provided 2019-12-31 criteria provided, single submitter clinical testing

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