Sequence Ontology

A shared vocabulary for biological sequence features and annotations

Home / Current release / SO:0002011

intragenic_variant

SO:0002011

Definition: A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence.

Comments and references

Requested by Pablo Cingolani, for use in SnpEff.

Definition references: SO:ke

Synonyms

ScopeValue
exactJannovar:intragenic_variant
exactintragenic variant
exactsnpEff:INTRAGENIC

Identifiers and subsets

Accession: SO:0002011

Persistent URL: http://purl.obolibrary.org/obo/SO_0002011

Alternate IDs: None

Subsets: None

Cross references: http://snpeff.sourceforge.net/SnpEff_manual.html

History summary

Term history is reconstructed from the Git-era ontology files by comparing ontology classes across revisions. Earlier SVN-era changes will be added at a future date.

First seen in Git-era editable history: 2016-12-05 in commit 92e3cae

Most recent Git-era change: 2021-07-12 in commit 795c410

Number of changes: 2

Ontology neighborhood diagram

Ontology neighborhood for SO:0002011 Ontology neighborhood graph for SO:0002011 intragenic_variant. Parent, child, and related nodes can be activated to open their term pages. SO:0001576 transcript_variant SO:0001576 transcript_variant SO:0002011 intragenic_variant SO:0002011 intragenic_variant
The local DAG shows nearby parent, child, and related terms. Each node links to its own term page.

Relationships

Parents

Children

None recorded in the current release neighborhood.

Change history

This timeline summarizes changes identified in SO’s GitHub commit history, including updates to labels, definitions, parent terms, synonyms, subsets, and obsoletion status. It is a best-effort reconstruction and may not include every change to a term. Since only history from GitHub is included at the moment, any term added before the migration from SVN to Git will show as being created in 2016. This will be addressed once SVN history is incorporated.

DateChangeSummaryEvidence
2021-07-12definition changedDefinition updated
Before: A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence.
After: A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence.
795c410
2016-12-05createdTerm introduced into the editable ontology history
Initial label: intragenic_variant
Initial definition captured.
Initial parent: SO:0001576
92e3cae