ClinVar Miner

Submissions for variant NM_004992.3(MECP2):c.*13C>T (rs782334844)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000443181 SCV000513578 likely benign not specified 2016-04-22 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Integrated Genetics/Laboratory Corporation of America RCV000443181 SCV001362154 benign not specified 2019-03-06 criteria provided, single submitter clinical testing Variant summary: MECP2 c.*13C>T is located in the untranslated mRNA region downstream of the termination codon. The variant allele was found at a frequency of 0.0001 in 200351 control chromosomes (gnomAD), including 6 hemizygotes. The observed variant frequency is approximately 12 fold of the estimated maximal expected allele frequency for a pathogenic variant in MECP2 causing Rett Syndrome phenotype (8.3e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.*13C>T in individuals affected with Rett Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.

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