Skip to main content

Table 1 sSNVs were annotated with a set of 10 optimized features spanning five distinct classes of infomration relevant to assessing the harmfulness of sSNVs

From: Computational identification of deleterious synonymous variants in human genomes using a feature-based approach

Feature name Description Type
Sequence feature
 DSP Mutation site distance to the nearest splice site Integer
Function regions annotation
 TFBS Whether the variant is in transcription factor binding site? Bool
Splicing
 MDE Minimum distance as a proportion of half the exon Numeric
 DVE Distance of the variant across the exon as a proportion Numeric
 ese-dens Density of neighborhood inference-exonic splicing enhancers hexamers in the exon sequence Numeric
 MES Max splice site score Numeric
 SR- SR-protein motifs lost Numeric
 dPSIZ The z-score of dPSI (the predicted change in percent-inclusion due to the variant, reported as the maximum across tissues) relative to the distribution of dPSI that are due to common variant Numeric
Conservation
 verPhyloP Vertebrate PhyloP at the mutation position at mutation position Numeric
Translation efficiency
 TE The tRNA adaptation index of the tRNA usage Numeric