Table 1.
The naming convention used to describe the sequence variants in the Ensembl Variation resources and dbSNP
| Ensembl variant consequences | dbSNP functional classes | SO ID | SO: Definition |
|---|---|---|---|
| Essential splice site | splice-3 | SO:0001574; SO:0001575 | A splice variant that changes the two base regions at the 3′ end of an intron; a splice variant that changes the two base regions at the 5′ end of an intron. |
| Stop gained | splice-5 | SO:0001587 | A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript. |
| Stop lost | nonsense | SO:0001578 | A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript. |
| Complex in/del | NA | SO:0001577 | A transcript variant with a complex INDEL—Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. |
| Frameshift coding | frameshift | SO:0001589 | A sequence variant, which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. |
| Non-synonymous coding | missense | SO:0001582; SO:0001652; SO:0001651; SO:0001583 | A codon variant that changes at least one base of the first codon of a transcript; an inframe non-synonymous variant that deletes bases from the coding sequence; an inframe non-synonymous variant that inserts bases into in the coding sequence; a sequence variant, where the change may be longer than three bases, and at least one base of a codon is changed, resulting in a codon that encodes for a different amino acid. |
| Splice site | NA | SO:0001630 | A sequence variant in which a change has occurred within the region of the splice site, either within 1–3 bases of the exon or 3–8 bases of the intron. |
| Partial codon | NA | SO:0001626 | A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed. |
| Synonymous coding | cds-synon | SO:0001567; SO:0001588 | A sequence variant where at least one base in the terminator codon is changed, but the terminator remains; a sequence variant where there is no resulting change to the encoded amino acid. |
| Coding unknown | NA | SO:0001580 | A sequence variant that changes the coding sequence. |
| Within mature miRNA | NA | SO:0001620 | A transcript variant located with the sequence of the mature miRNA. |
| 5′ UTR | untranslated_5 /UTR-5 | SO:0001623 | A UTR variant of the 5′ UTR. |
| 3′ UTR | untranslated_3 /UTR-3 | SO:0001624 | A UTR variant of the 3′ UTR. |
| Intronic | intron | SO:0001627 | A transcript variant occurring within an intron. |
| NMD transcript | SO:0001621 | A variant in a transcript that is the target of NMD. | |
| Within non-coding gene | ncRNA | SO:0001619 | A transcript variant of a non-coding RNA gene. |
| Upstream | near-gene-5 | SO:0001636; SO:0001635 | A sequence variant located within 2 KB 5′ of a gene; a sequence variant located within 5 KB 5′ of a gene. |
| Downstream | near-gene-3 | SO:0001634; SO:0001633 | A sequence variant located within a half KB of the end of a gene; a sequence variant located within 5 KB of the end of a gene. |
| Regulatory region | NA | SO:0001566 | A sequence variant located within a regulatory region. |
| Transcription factor binding motif | NA | SO:0001782 | A sequence variant located within a transcription factor-binding site. |
| Intergenic | intergenic | SO:0001628 | A sequence variant located in the intergenic region, between genes. |
SO identifiers and descriptions were obtained from MISO ( www.sequenceontology.org/miso/ ).