Interpret consequence labels (CSQN)

For each genetic variant, TransVar assigns a consequence label with CSQN tag. The consequence label sometimes explains the behaviour of the output, e.g., the missing of protein level representation due to the loss of splice site.

The consequence label is in the following alphabet:


label interpretation
Synonymous Variation in protein-coding sequence
  results in the same protein sequence
Missense Single or multiple amino acid
  substitution to coding gene (1-1)
MultiAAMissense In-frame multiple amino acid replacement
  (m to n, either m>1 or n>1)
Nonsense Introduction of stop codon by single,
  multiple amino acid substitution or
  in-frame insertions/deletions

Coding Start/Stop

label interpretation
CdsStartSNV SNV at coding start
CdsStopSNV SNV at coding stop
CdsStartDeletion deletion of coding start
CdsStopDeletion deletion of coding stop

Coding Insertion/Deletion

label interpretation
Frameshift Frameshift mutation to a coding gene
InFrameDeletion In-frame deletion to a coding gene
InFrameInsertion In-frame insertion to a coding gene


label interpretation
IntronicSNV Intronic single nucleotide variation
IntronicDeletion Intronic deletion
IntronicInsertion Intronic insertion
IntronicBlockSubstitutio Intronic block substitution


label interpretation
IntergenicSNV Intergenic single nucleotide variation
IntergenicDeletion Intergenic deletion
IntergenicInsertion Intergenic insertion
IntergenicBlockSubstitution Intergenic block substitution

Splice site

label interpretation
SpliceDonorDeletion Deletion occurs to splice donor
SpliceAcceptorDeletion Deletion occurs to splice acceptor
SpliceDonorSNV Genetic variation at splice donor
SpliceAcceptorSNV Genetic variation at splice acceptor
SpliceDonorBlockSubstitution Block substitution occurs at splice donor
SpliceAcceptorBlockSubstitution Block substitution occurs at splice acceptor
SpliceDonorInsertion Insertion at splice donor
SpliceAcceptorInsertion Insertion at splice acceptor


label interpretation
Unclassified Unclassified