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Table 2 Gene and transcript-related fields reported by the VEP

From: The Ensembl Variant Effect Predictor

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