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Table 6 Co-located variant-related fields reported by the VEP

From: The Ensembl Variant Effect Predictor

Property Description
Variant ID External identifier for variant co-located with input, e.g., rsID from dbSNP
Somatic Somatic status of co-located variant
GMAF Global minor allele and frequency of co-located variant from combined 1000 Genomes phase 3 populations
Other frequencies Frequency data from continental level 1000 Genomes phase 3 data and two NHLBI–Exome Sequencing Project populations
Clinical significance Clinical significance status of co-located variant as reported by ClinVar
Phenotype Flag indicating known association with a phenotype or disease
PubMed ID NCBI PubMed IDs of publications citing co-located variant