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 |