Table 2. Detailed effect list from SnpEff.

Effect	Note
INTERGENIC	The variant is in an intergenic region
UPSTREAM	Upstream of a gene (default length: 5K bases)
UTR_5_PRIME	Variant hits 5′UTR region
UTR_5_DELETED	The variant deletes an exon which is in the 5′UTR of the transcript
START_GAINED	A variant in 5′UTR region produces a three base sequence that can be a START codon.
SPLICE_SITE_ACCEPTOR	The variant hits a splice acceptor site (defined as two bases before exon start, except for the first exon).
SPLICE_SITE_DONOR	The variant hits a Splice donor site (defined as two bases after coding exon end, except for the last exon).
START_LOST	Variant causes start codon to be mutated into a non-start codon.
SYNONYMOUS_START	Variant causes start codon to be mutated into another start codon.
CDS	The variant hits a CDS.
GENE	The variant hits a gene.
TRANSCRIPT	The variant hits a transcript.
EXON	The vairant hist an exon.
EXON_DELETED	A deletion removes the whole exon.
NON_SYNONYMOUS_CODING	Variant causes a codon that produces a different amino acid
SYNONYMOUS_CODING	Variant causes a codon that produces the same amino acid
FRAME_SHIFT	Insertion or deletion causes a frame shift
CODON_CHANGE	One or many codons are changed
CODON_INSERTION	One or many codons are inserted
CODON_CHANGE_PLUS_CODON_INSERTION	One codon is changed and one or many codons are inserted
CODON_DELETION	One or many codons are deleted
CODON_CHANGE_PLUS_CODON_DELETION	One codon is changed and one or more codons are deleted
STOP_GAINED	Variant causes a STOP codon
SYNONYMOUS_STOP	Variant causes stop codon to be mutated into another stop codon.
STOP_LOST	Variant causes stop codon to be mutated into a non-stop codon
INTRON	Variant hist and intron. Technically, hits no exon in the transcript.
UTR_3_PRIME	Variant hits 3′UTR region
UTR_3_DELETED	The variant deletes an exon which is in the 3′UTR of the transcript
DOWNSTREAM	Downstream of a gene (default length: 5K bases)
INTRON_CONSERVED	The variant is in a highly conserved intronic region
INTERGENIC_CONSERVED	The variant is in a highly conserved intergenic region