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:

General

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

Intronic

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

Intergenic

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

Others

label	interpretation
Unclassified	Unclassified