ClinVar Miner

Submissions for variant NM_001110792.2(MECP2):c.870C>T (p.Ala290=) (rs61750248)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Integrated Genetics/Laboratory Corporation of America RCV000589640 SCV000698545 benign not provided 2016-10-11 criteria provided, single submitter clinical testing Variant summary: The MECP2 c.834C>T (p.Ala278Ala) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predict no significant impact on normal splicing and ESE finder predicts alterations to ESE binding, although these predictions have yet to be functionally assessed. The variant of interest has been observed in the large, broad control population, ExAC, with an allele frequency of 49/85676 (18 hemizygotes, 1/1748), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic MECP2 variant of 1/120481. In addition, multiple publications and a reputable database has cited the variant as "benign/silent polymorphism." Therefore, the variant of interest has been classified as Benign.
Ambry Genetics RCV000716695 SCV000847538 likely benign History of neurodevelopmental disorder 2016-08-23 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign;In silico models in agreement (benign)
Invitae RCV001080240 SCV001003075 benign Severe neonatal-onset encephalopathy with microcephaly 2019-12-31 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000589640 SCV001150512 likely benign not provided 2019-06-01 criteria provided, single submitter clinical testing
RettBASE RCV000168694 SCV000188255 benign not specified 2010-03-10 no assertion criteria provided curation

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