Table 4 List of consequence types in the transcript variation table
Consequence type | Effect | Sequence location |
|---|---|---|
Stop gained | causes a gain of a stop codon | coding sequence of the peptide |
Stop lost | causes a loss of a stop codon | coding sequence of the peptide |
complex InDel | change in nucleic acid | Indel spanning exon/intron or CDS/UTR border |
Frameshift coding | causes a frameshift of the reading frame | affects the coding sequence of the peptide |
Stop gained, frameshift coding | multi-allelic variant that introduces a stop codon or causes a frameshift | affects the coding sequence |
Non-synonymous coding | causes an amino acid change | coding sequence of the peptide |
Stop gained, splice site | causes a gain of a stop codon | 1-3 bps into an exon |
Stop lost, splice site | causes a loss of a stop codon | 1-3 bps into an exon |
Frameshift coding, splice site | causes a frameshift | 1-3 bps into an exon |
stop gained, Frameshift coding, splice site | Multi-allelic variant that introduces a stop codon or causes a frameshift | 1-3 bps into an exon |
Non-Synonymous coding, splice site | causes an amino acid change | 1-3 bps into an exon |
Synonymous coding | change in nucleic acid but no change in amino acid | coding sequence of the peptide |
Splice site, synonymous coding | change in nucleic acid but no change in amino acid | 1-3 bps into an exon |
Regulatory region | change in nucleic acid | regulatory region annotated by Ensembl |
Within mature miRNA | change in nucleic acid | within mature miRNA |
5' UTR | change in nucleic acid | In 5' UTR |
Splice site, 5' UTR | change in nucleic acid | 1-3 bps into a 5' UTR exon |
3' UTR | change in nucleic acid | In 3' UTR |
Splice site, 3' UTR | change in nucleic acid | 1-3 bps into a 3' UTR exon |
Intronic | change in nucleic acid | In intron |
Essential splice site, intronic | change in nucleic acid | in the first 2 or the last 2 base pairs of an intron |
Splice site, intronic | change in nucleic acid | 3-8 bps into an intron |
Upstream | change in nucleic acid | Within 5 kb upstream of the 5'-end of a transcript |
Downstream | change in nucleic acid | Within 5 kb downstream of the 3'-end of a transcript |
Within non-coding gene | change in nucleic acid | Within non-coding gene |
Intergenic | change in nucleic acid | More than 5 kb away from a transcript |