By default VEP will tell you the consequences for every transcript affected by a variant. You may wish to prioritise your analysis to only the most important or well supported transcripts for each gene, and VEP provides information to help you do that.
VEP transcript flags in the web interface
A number of flags are added to human transcripts in Ensembl to indicate their quality and their biological relevance. All of these can be added to your VEP annotation, whether you use the web tool, the REST service or the command-line tool.
You can find the most biologically relevant transcript for a gene in the MANE Select (Matched Annotation between NCBI and EBI) set. These are agreed by both NCBI and Ensembl to be the most biologically relevant transcripts, and also perfectly match between the RefSeq and Ensembl/GENCODE annotation. If this is not available for your gene of interest, you can select from the APPRIS annotation, which annotates the most biologically relevant Principal (P1-5) or Alternative (ALT1-2) transcripts.
A guide to the quality of a transcript can be obtained from the Transcript Support Level (TSL) a score from one (best) to five (worst).
If you select these options the flags will be displayed in your output. You can then use these with the VEP filtering options to reduce your output and prioritise your prefered transcript sets.