ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.771C>G (p.Val257=) (rs782027467)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000457731 SCV000556751 benign Severe neonatal-onset encephalopathy with microcephaly 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000781522 SCV000919621 benign not specified 2018-09-04 criteria provided, single submitter clinical testing Variant summary: MECP2 c.735C>G alters a conserved nucleotide resulting in a synonymous change. Several computational tools predict a significant impact on normal splicing: five predict the variant strengthens a cryptic 5 prime donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00013 in 178616 control chromosomes, predominantly within the Latino subpopulation at a frequency of 0.00087 in the gnomAD database. This frequency within Latino control individuals is approximately 104-fold above 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 a benign polymorphism found primarily in populations of Latino origin. To our knowledge, no occurrence of c.735C>G in individuals affected with Rett Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.

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