categorizing VEP annotations into consequences

Question

[storm1907]

Hello,

I need to run downstream analysis where counts of functional and synonymous variants are needed.

I have VCFs annotated with VEP.

When annotating variants with VEP, in is not quite understandable, which outputs could be counted as synonymous and functional. It is, of course, clear with missense, frameshift, splice and synonymous variants.

But what to do with other VEP annotated types? Do I count stop retained and inframe variants as synonymous? Or take them out from analysis? Annotation list is below.

Thank you!

variants_effect_3_prime_UTR_variant
variants_effect_5_prime_UTR_premature_start_codon_gain_variant
variants_effect_5_prime_UTR_variant
variants_effect_conservative_inframe_deletion
variants_effect_conservative_inframe_insertion
variants_effect_disruptive_inframe_deletion
variants_effect_disruptive_inframe_insertion
variants_effect_downstream_gene_variant
variants_effect_frameshift_variant
variants_effect_initiator_codon_variant
variants_effect_intron_variant
variants_effect_missense_variant
variants_effect_non_coding_transcript_exon_variant
variants_effect_non_coding_transcript_variant
variants_effect_splice_acceptor_variant
variants_effect_splice_donor_variant
variants_effect_splice_region_variant
variants_effect_start_lost
variants_effect_stop_gained
variants_effect_stop_lost
variants_effect_stop_retained_variant
variants_effect_synonymous_variant
variants_effect_upstream_gene_variant

Answer 1

[Emily]

You could perhaps look at the ranking order and IMPACT classifications in the documentation.