| transcript_ablation |
NA |
A feature ablation whereby the deleted region includes a transcript feature |
SO:0001893 |
Transcript ablation |
HIGH |
| splice_acceptor_variant |
splice-3 |
A splice variant that changes the 2 base region at the 3' end of an intron |
SO:0001574 |
Splice acceptor variant |
HIGH |
| splice_donor_variant |
splice-5 |
A splice variant that changes the 2 base region at the 5' end of an intron |
SO:0001575 |
Splice donor variant |
HIGH |
| stop_gained |
nonsense |
A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript |
SO:0001587 |
Stop gained |
HIGH |
| frameshift_variant |
frameshift |
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 |
SO:0001589 |
Frameshift variant |
HIGH |
| stop_lost |
stop-loss |
A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript |
SO:0001578 |
Stop lost |
HIGH |
| start_lost |
NA |
A codon variant that changes at least one base of the canonical start codon |
SO:0002012 |
Start lost |
HIGH |
| transcript_amplification |
NA |
A feature amplification of a region containing a transcript |
SO:0001889 |
Transcript amplification |
HIGH |
| inframe_insertion |
NA |
An inframe non synonymous variant that inserts bases into in the coding sequence |
SO:0001821 |
Inframe insertion |
MODERATE |
| inframe_deletion |
NA |
An inframe non synonymous variant that deletes bases from the coding sequence |
SO:0001822 |
Inframe deletion |
MODERATE |
| missense_variant |
missense |
A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved |
SO:0001583 |
Missense variant |
MODERATE |
| protein_altering_variant |
NA |
A sequence_variant which is predicted to change the protein encoded in the coding sequence |
SO:0001818 |
Protein altering variant |
MODERATE |
| splice_region_variant |
NA |
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 |
SO:0001630 |
Splice region variant |
LOW |
| splice_donor_5th_base_variant |
NA |
A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript |
SO:0001787 |
Splice donor 5th base variant |
LOW |
| splice_donor_region_variant |
NA |
A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron) |
SO:0002170 |
Splice donor region variant |
LOW |
| splice_polypyrimidine_tract_variant |
NA |
A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17) |
SO:0002169 |
Splice polypyrimidine tract variant |
LOW |
| incomplete_terminal_codon_variant |
NA |
A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed |
SO:0001626 |
Incomplete terminal codon variant |
LOW |
| start_retained_variant |
NA |
A sequence variant where at least one base in the start codon is changed, but the start remains |
SO:0002019 |
Start retained variant |
LOW |
| stop_retained_variant |
NA |
A sequence variant where at least one base in the terminator codon is changed, but the terminator remains |
SO:0001567 |
Stop retained variant |
LOW |
| synonymous_variant |
coding-synon |
A sequence variant where there is no resulting change to the encoded amino acid |
SO:0001819 |
Synonymous variant |
LOW |
| coding_sequence_variant |
NA |
A sequence variant that changes the coding sequence |
SO:0001580 |
Coding sequence variant |
MODIFIER |
| mature_miRNA_variant |
NA |
A transcript variant located with the sequence of the mature miRNA |
SO:0001620 |
Mature miRNA variant |
MODIFIER |
| 5_prime_UTR_variant |
untranslated-5 |
A UTR variant of the 5' UTR |
SO:0001623 |
5 prime UTR variant |
MODIFIER |
| 3_prime_UTR_variant |
untranslated-3 |
A UTR variant of the 3' UTR |
SO:0001624 |
3 prime UTR variant |
MODIFIER |
| non_coding_transcript_exon_variant |
NA |
A sequence variant that changes non-coding exon sequence in a non-coding transcript |
SO:0001792 |
Non coding transcript exon variant |
MODIFIER |
| intron_variant |
intron |
A transcript variant occurring within an intron |
SO:0001627 |
Intron variant |
MODIFIER |
| NMD_transcript_variant |
NA |
A variant in a transcript that is the target of NMD |
SO:0001621 |
NMD transcript variant |
MODIFIER |
| non_coding_transcript_variant |
NA |
A transcript variant of a non coding RNA gene |
SO:0001619 |
Non coding transcript variant |
MODIFIER |
| upstream_gene_variant |
near-gene-5 |
A sequence variant located 5' of a gene |
SO:0001631 |
Upstream gene variant |
MODIFIER |
| downstream_gene_variant |
near-gene-3 |
A sequence variant located 3' of a gene |
SO:0001632 |
Downstream gene variant |
MODIFIER |
| TFBS_ablation |
NA |
A feature ablation whereby the deleted region includes a transcription factor binding site |
SO:0001895 |
TFBS ablation |
MODIFIER |
| TFBS_amplification |
NA |
A feature amplification of a region containing a transcription factor binding site |
SO:0001892 |
TFBS amplification |
MODIFIER |
| TF_binding_site_variant |
NA |
A sequence variant located within a transcription factor binding site |
SO:0001782 |
TF binding site variant |
MODIFIER |
| regulatory_region_ablation |
NA |
A feature ablation whereby the deleted region includes a regulatory region |
SO:0001894 |
Regulatory region ablation |
MODERATE |
| regulatory_region_amplification |
NA |
A feature amplification of a region containing a regulatory region |
SO:0001891 |
Regulatory region amplification |
MODIFIER |
| feature_elongation |
NA |
A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence |
SO:0001907 |
Feature elongation |
MODIFIER |
| regulatory_region_variant |
NA |
A sequence variant located within a regulatory region |
SO:0001566 |
Regulatory region variant |
MODIFIER |
| feature_truncation |
NA |
A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence |
SO:0001906 |
Feature truncation |
MODIFIER |
| intergenic_variant |
NA |
A sequence variant located in the intergenic region, between genes |
SO:0001628 |
Intergenic variant |
MODIFIER |
