The following effect terms that are recognized are listed here, though each group typically uses only a few of these, such as the core terms missense, frameshift, and synonymous. The listing here is periodically updated to include all SnpEff effect prediction terms, but let us know if we are missing any. The terms are case-insensitive. If multiple terms are used (separated by “|” or “&” or “,” or “/”), each effect term is considered and the one with the highest severity is chosen.
- 2kb_upstream_variant
- 3_prime_utr_truncation
- 3_prime_utr_variant
- 5_prime_utr_premature_start_codon_gain_variant
- 5_prime_utr_truncation
- 5_prime_utr_variant
- 500B_downstream_variant
- 5KB_downstream_variant
- 5KB_upstream_variant
- absence_of_heterozygosity
- cds
- chromosome
- chromosome_large_deletion
- coding
- coding-near-splice
- coding-notmod3
- coding-notmod3-near-splice
- coding_sequence_variant
- coding-synonymous
- coding-synonymous-near-splice
- codon_change
- codon_change_plus_codon_del
- codon_change_plus_codon_deletion
- codon_change_plus_codon_ins
- codon_change_plus_codon_insertion
- codon_del
- codon_deletion
- codon_ins
- codon_insertion
- complex_change_in_transcript
- conservative_inframe_deletion
- conservative_inframe_insertion
- conserved_intergenic_variant
- conserved_intron_variant
- del
- deletion
- disruptive_inframe_deletion
- disruptive_inframe_insertion
- downstream
- downstream_gene_variant
- dup
- duplication
- exon
- exon_deleted
- exon_loss_variant
- exon_variant
- exonic_splicing
- frameshift
- frame_shift
- frameshift deletion
- frameshift_deletion
- frameshift insertion
- frameshift_insertion
- frameshift-near-splice
- frameshift substitution
- frameshift_variant
- frame_shift
- gene
- gene_variant
- incomplete_terminal_codon_variant
- in-frame
- inframe_codon_gain
- inframe_codon_loss
- inframe_deletion
- inframe_insertion
- initiator_codon_change
- initiator_codon_variant
- intergenic
- intergenic_conserved
- intergenic_region
- intragenic
- intragenic_variant
- intron
- intron_conserved
- intron_variant
- intronic
- LOH
- loss_of_heterozygosity
- mature_mir._variant
- mature_mirna_variant
- missense
- missense-near-splice
- missense_variant
- ncRNA_exonic
- ncRNA_intronic
- ncRNA_splicing
- nc_transcript_variant
- non_coding_transcript_variant
- near-gene-3
- near-gene-5
- noncoding
- non_canonical_start_codon
- non_coding_exon_variant
- non_coding_transcript_exon_variant
- nonframeshift
- nonframeshift deletion
- nonframeshift_deletion
- nonframeshift insertion
- nonframeshift_insertion
- nonframeshift substitution
- no-stop
- nonsense
- nonsynonymous
- nonsynonymous snv
- nonsynonymous_snv
- non_synonymous_coding
- non_synonymous_codon
- non_synonymous_start
- non_synonymous_stop
- nsc
- protein_altering_variant
- protein_protein_contact
- rare_amino_acid
- rare_amino_acid_variant
- regulation
- regulatory_region_variant
- sequence_feature
- splice-3
- spice-5
- splice_acceptor_variant
- splice_branch_variant
- splice_donor_variant
- splice_region_variant
- splice_retained_variant
- splice_site_acceptor
- splice_site_branch
- splice_site_branch_u12
- splice_site_donor
- splice_site_region
- splicing
- start_gained
- start_lost
- start_retained
- start_retained_variant
- stopgain
- stop_gained
- stop-gained
- stop-gained-near-splice
- stopgain snv
- stopgain_snv
- stoploss
- stop_lost
- stop-lost
- stop_retained
- stop_retained_variant
- stop-lost-near-splice
- stoploss snv
- stoploss_snv
- stop_retained_variant
- structural_interaction_variant
- synonymous
- synonymous_coding
- synonymous_codon
- synonymous_start
- synonymous_stop
- synonymous_stop
- synonymous snv
- synonymous_snv
- synonymous_variant
- tf_binding_site_variant
- TFBS_ablation
- transcript
- transcript_ablation
- transcript_amplification
- transcript_variant
- upstream
- upstream_gene_variant
- utr3
- utr-3
- utr_3_deleted
- utr_3_prime
- utr5
- utr-5
- utr_5_deleted
- utr_5_prime
- unknown
- a blank, space, “.” and “-” allowed, interpreted as zero in calculation of effect severity