Table 2 Gene and transcript-related fields reported by the VEP
Property | Description |
|---|---|
Gene ID | Ensembl stable identifier for affected gene |
Gene symbol | Common name for gene, e.g., from HGNC |
Transcript ID | Ensembl stable identifier for affected transcript |
RefSeq ID | NCBI RefSeq identifier for affected transcript |
CCDS ID | Consensus coding sequence (CCDS) identifier uniting Havana, Ensembl, and NCBI |
Biotype | GENCODE biotype of affected transcript |
cDNA coordinates | Coordinates of input variant in unprocessed cDNA |
CDS coordinates | Coordinates of input variant in processed coding sequence (CDS) |
Distance | Distance to transcript if variant falls outside transcript boundaries |
Consequence type | SO consequence type of input variant allele on transcript |
Exon | Number(s) of affected exon(s) |
Intron | Number(s) of affected intron(s) |
TSL | Transcript Support Level (TSL) highlights well-supported and poorly supported transcript models |
APPRIS | Annotation principle splice isoforms (APPRIS) is a system to annotate alternatively spliced transcripts based on a range of computational methods, assigning primary and alternative statuses to transcripts |
HGVS | HGVS notations for input variant relative to the coding sequence |
Phenotype | Flag indicating known association with a phenotype or disease |