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 protein-coding gene (1 to 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 ---	-----
CdsStartLoss	Loss of coding start
CdsStopLoss	Loss of coding stop
--- Coding Insertion/Deletion ---	-----
Frameshift	Frameshift mutation to a protein-coding gene
InFrameDeletion	In-frame deletion to a protein-coding gene
InFrameInsertion	In-frame insertion to a protein-coding gene
--- Intronic ---	-----
IntronicSNV	Intronic single nucleotide variation
IntronicDeletion	Intronic deletion
IntronicInsertion	Intronic insertion
IntronicBlockSubstitution	Intronic block substitution
--- Intergenic ---	-----
IntergenicSNV	Intergenic single nucleotide variation
IntergenicDeletion	Intergenic deletion
IntergenicInsertion	Intergenic insertion
IntergenicBlockSubstitution	Intergenic block substitution
--- Splice site ---	-----
SpliceDonorDeletion	Deletion occurs to splice donor
SpliceAcceptorDeletion	Deletion occurs to splice acceptor
SpliceDonorSNV	Single-nucleotide variation at splice donor
SpliceAcceptorSNV	Single-nucleotide 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
--- Others ---	-----
Unclassified	Unclassified due to mostly mal-formated input