ClinVar Miner

Submissions for variant NM_000399.5(EGR2):c.174C>T (p.Gly58=) (rs143793213)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000235368 SCV000293636 uncertain significance not provided 2015-12-10 criteria provided, single submitter clinical testing The c.174 C>T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.174 C>T variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Several in-silico splice prediction models predict that c.174 C>T creates a cryptic donor site which may supplant the natural donor site and 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.
Illumina Clinical Services Laboratory,Illumina RCV001094068 SCV000363340 likely benign Charcot-Marie-Tooth disease, demyelinating, type 1d 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 RCV000556157 SCV000636228 benign Charcot-Marie-Tooth disease, type I 2019-12-31 criteria provided, single submitter clinical testing

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