Skip to content

Commit

Permalink
Change user-facing references to dataset to say "v4 SVs"
Browse files Browse the repository at this point in the history
This includes the dataset ID `gnomad_sv_v4` itself as that appears in URLs.
  • Loading branch information
phildarnowsky-broad committed Oct 27, 2023
1 parent 5d9028d commit c1a11c2
Show file tree
Hide file tree
Showing 31 changed files with 378 additions and 378 deletions.
8 changes: 4 additions & 4 deletions browser/help/topics/structural-variants/sv-effect-overview.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,17 +14,17 @@ The functional consequence per SV was determined in the order below:
### Main functional consequences

1. ![](https://placehold.it/15/D43925/000000?text=+) **Predicted loss-of-function (pLoF)**: SV is predicted to delete the gene or truncate the gene product.
2. ![](https://placehold.it/15/7459B2/000000?text=+) **Intragenic exonic duplication (IED)**: SV is predicted to result in duplicated exons within the gene, without extending beyond the boundaries of the open reading frame. (New in gnomAD v3)
3. **Partial exon duplication (PED)**: SV is predicted to duplicate part of one or more exons without resulting in a whole-gene copy gain. (New in gnomAD v3)
2. ![](https://placehold.it/15/7459B2/000000?text=+) **Intragenic exonic duplication (IED)**: SV is predicted to result in duplicated exons within the gene, without extending beyond the boundaries of the open reading frame. (New in gnomAD v4)
3. **Partial exon duplication (PED)**: SV is predicted to duplicate part of one or more exons without resulting in a whole-gene copy gain. (New in gnomAD v4)
4. ![](https://placehold.it/15/2376B2/000000?text=+) **Copy gain (CG)**: SV is predicted to result in an entire additional intact copy of the gene.

### Other consequences

4. **Transcription start site duplication**: SV is predicted to result in a duplication of a transcription start site but not result in any other, more severe consequences. (New in gnomAD v3).
4. **Transcription start site duplication**: SV is predicted to result in a duplication of a transcription start site but not result in any other, more severe consequences. (New in gnomAD v4).
5. **MCNV overlap**: MCNV overlaps one or more protein-coding exons; exact consequence depends on the number of copies and their orientation.

6. **Partial duplication**: SV is predicted to partially duplicate the gene while leaving the original copy of the gene intact.
7. **Exonic breakend**: breakend localizes to exonic locus, but consequence is unclear as SV is incompletely resolved. (New in gnomAD v3).
7. **Exonic breakend**: breakend localizes to exonic locus, but consequence is unclear as SV is incompletely resolved. (New in gnomAD v4).
8. **UTR**: SV does not directly disrupt coding sequence, but overlaps one of the gene's untranslated regions (UTRs).
9. **Promoter**: SV does not directly disrupt coding sequence or promoter, but is within 2kb of the gene's transcription start site.
10. **Inversion span**: gene is entirely spanned by an inversion SV without being directly disrupted.
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -6510,37 +6510,37 @@ exports[`ConstraintTable with "gnomad_sv_r2_1_non_neuro" dataset selected with a
</p>
`;

exports[`ConstraintTable with "gnomad_sv_r3" dataset selected and gene with available constraint has no unexpected changes 1`] = `
exports[`ConstraintTable with "gnomad_sv_r4" dataset selected and gene with available constraint has no unexpected changes 1`] = `
<p>
Constraint not yet available for gnomAD v3.
</p>
`;

exports[`ConstraintTable with "gnomad_sv_r3" dataset selected and transcript with available constraint has no unexpected changes 1`] = `
exports[`ConstraintTable with "gnomad_sv_r4" dataset selected and transcript with available constraint has no unexpected changes 1`] = `
<p>
Constraint not yet available for gnomAD v3.
</p>
`;

exports[`ConstraintTable with "gnomad_sv_r3" dataset selected with a minimal gene has no unexpected changes 1`] = `
exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a minimal gene has no unexpected changes 1`] = `
<p>
Constraint not yet available for gnomAD v3.
</p>
`;

exports[`ConstraintTable with "gnomad_sv_r3" dataset selected with a minimal transcript has no unexpected changes 1`] = `
exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a minimal transcript has no unexpected changes 1`] = `
<p>
Constraint not yet available for gnomAD v3.
</p>
`;

exports[`ConstraintTable with "gnomad_sv_r3" dataset selected with a mitochondrial gene has no unexpected changes 1`] = `
exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a mitochondrial gene has no unexpected changes 1`] = `
<p>
Constraint not yet available for gnomAD v3.
</p>
`;

exports[`ConstraintTable with "gnomad_sv_r3" dataset selected with a mitochondrial transcript has no unexpected changes 1`] = `
exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a mitochondrial transcript has no unexpected changes 1`] = `
<p>
Constraint not yet available for gnomAD v3.
</p>
Expand Down
10 changes: 5 additions & 5 deletions browser/src/DatasetSelector.tsx
Original file line number Diff line number Diff line change
Expand Up @@ -594,11 +594,11 @@ const DatasetSelector = withRouter(({ datasetOptions, history, selectedDataset }
label: 'More datasets',
children: [
{
id: 'gnomad_sv_r3',
label: labelForDataset('gnomad_sv_r3'),
url: datasetLink('gnomad_sv_r3'),
description: `${sampleCounts.gnomad_sv_r3.total.toLocaleString()} samples`,
childReferenceGenome: referenceGenome('gnomad_sv_r3'),
id: 'gnomad_sv_r4',
label: labelForDataset('gnomad_sv_r4'),
url: datasetLink('gnomad_sv_r4'),
description: `${sampleCounts.gnomad_sv_r4.total.toLocaleString()} samples`,
childReferenceGenome: referenceGenome('gnomad_sv_r4'),
},
{
id: 'gnomad_sv_r2_1',
Expand Down
Loading

0 comments on commit c1a11c2

Please sign in to comment.