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Table 1 CAVA variant classification system

From: CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting

Class Description
SG Stop-gain (nonsense) variant caused by base substitution
ESS Any variant that alters essential splice-site base (+1, +2, −1, −2)
SS5 Any variant that alters +5 splice-site base but not an ESS base
SS Any variant that alters splice-site base within the first eight intronic bases flanking exon (i.e., +8 to −8) but not an ESS or SS5 base
EE Variant that alters the first or last three bases of an exon (i.e., the exon end), but not the frame of the coding sequence
FS Frameshifting insertion and/or deletion. It alters length and frame of coding sequence
IM Variant that alters initiating methionine start codon
SL Variant that causes a stop-loss (i.e., the stop codon is altered)
IF Inframe insertion and/or deletion. It alters length but not frame of coding sequence
NSY Nonsynonymous variant. It alters amino acid(s) but not coding sequence length
SY Synonymous variant. It does not alter amino acid or coding sequence length
INT Any variant in an intron that does not alter splice-site bases
5PU Any variant in 5′ untranslated region
3PU Any variant in 3′ untranslated region
  1. A variant can only have one CAVA class. If a variant could potentially be included in more than one class, the first class in the list is assigned. For example, a frameshifting deletion that alters the start codon would be CAVA class FS (not IM). Nonsynonymous is also known as missense. Stop-gain is also known as nonsense