in their script, variant_effect_predictor.pl

in config section you can set that value (db_version):

# sets up configuration hash that is used throughout the script
sub configure {
...
    # DB options
    'species=s',               # species e.g. human, homo_sapiens
    'registry=s',              # registry file
    'host=s',                  # database host
    'port=s',                  # database port
    'user=s',                  # database user name
    'password=s',              # database password
    'db_version=i',            # Ensembl database version to use e.g. 62
    'genomes',                 # automatically sets DB params for e!Genomes
...