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rs200643387

  • Conflicting interpretations of pathogenicity

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Description

Variant classified as Uncertain Significance - Favor Benign. The p.Ala292Ser in CASQ2 has not been reported in individuals with cardiomopathy, but has been repo rted in 0.2% (13/6602) of Finnish chromosomes by the Exome Aggregation Consortiu m (ExAC, http://exac.broadinstitute.org; dbSNP rs200643387). Computational predi ction tools and conservation analysis do not provide strong support for or again st and impact to the protein. In summary, while the clinical significance of the p.Ala292Ser variant is uncertain, its frequency suggests that it is more likely to be benign.

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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

Reference Allele

C


Alternative Allele

A

Chromosome

1


Location

115705257


Variant Type

SNP

Genes

ClinVar

Name

NM_001232.4(CASQ2):c.874G>T (p.Ala292Ser)


Allele

A


Clinical Significance

Conflicting interpretations of pathogenicity

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