AlleleMolecularConsequenceStatement

Scope and Usage

Molecular consequence statements typically describe the type of variation the allele represents (e.g. a deletion or insertion or translocation), the type of genomic or transcript feature the allele affects (e.g. that it occurs in a 3' UTR, or an exon), or its impact on the structure or processing of a gene (e.g. that it generates a copy number variation, results in a lost stop codon, disrupts a slice site, or causes a frameshift elongation). Molecular Consequence statements do not include predictions about the impact a variation might have on the function of an encoded gene product.

Example of usage. Molecular consequence statements are produced by software such as Annovar (http://annovar.openbioinformatics.org), SnpEff (http://snpeff.sourceforge.net) or Variant Effect Predictor (http://www.ensembl.org/vep), and often take the form of annotation of a variant with a term from the sequence ontology such as 'missense variant', 'frameshift variant', 'splice-site variant', 'frameshift elongation', 'substitution', 'inversion'.

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