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


Chen et al. BMC Genomics 2010 11:293   doi:10.1186/1471-2164-11-293

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