Variant Details Somatic CNV¶
To open the variant details page, click 'View details' button on your chosen variant in the variant list.
On this page you can:
- Review the QC information for a variant
- Review additional annotations such as internal GeL population frequencies
- Link out to IGV
- Flag a variant
- Add a variant for export
- Add a comment and or classification to a variant
Variant and Quality Information¶
This panel allows you to view variant coordinates and quality metrics. You can also link out to view the variant in IGV
Key
| # | Section | Description |
|---|---|---|
| 1 | GRCh38 coordinates | The chromosome and position for each breakpoint of the variant. |
| 2 | Chromosomal bands | The chromosomal band(s) overlapping this variant. |
| 3 | Variant type | Variant type for this CNV: Gain, Loss or copy neutral loss of heterozygosity (LOH) |
| 4 | Confidence | For Canvas calls, “HC” and “LC” indicate high and low confidence variants, with the Canvas quality score shown. Quality scores for CNVs take into account: i. bin count — longer CNVs will be given higher score ii. coverage for CNV should fit to predicted coverage — sub-clonal CNVs will have low score iii. distance between current copy number solution and the next one — this distance will be low for high copy numbers where the relative fold change between neighbouring copy number states is small. Therefore copy number variants with a high number of copies (such as focal amplifications) may be designated as low confidence where the specific copy number is uncertain. Confidence in the variant call based on the quality score assigned by the variant caller (Canvas). |
| 5 | Size (KB) | Size of the CNV in kilobases. |
| 6 | Copy number | Copy number for this CNV. |
| 7 | View in IGV | View this region in IGV. |
Interpretation¶
This panel allows you to flag, classify, comment and export variants. Please refer to the Recording Interpretation documentation for more details.
Gene information¶
This panel allows you to view information about the domained genes overlapping this variant.
It includes:
- Mode of action as listed in Cancer Gene Census (e.g. Oncogene, Tumor suppressor)
- Domain as assigned by the Genomics England pipeline (see Cancer Genome Analysis Guide)
- Matching clinical indications from the NHS National Genomic Test Directory (that also match the Clinical Indication Group of the patient).
Transcripts
By default, the canonical transcript is shown. But additional transcripts can be viewed by clicking Show alternative transcripts.
Tip
Genes can be selected by expanding the list under each domain on the left of the panel. The number highlighted next to each domain is a count of the genes.
Key
| # | Section | Description |
|---|---|---|
| 1 | Affected gene | HGNC Gene symbol. |
| 2 | Mode of action | Mode of action as defined in Cancer Gene Census (Oncogene, Tumor Suppressor gene, Ambiguous) |
| 3 | Domain | Domain as assigned by the Genomics England pipeline (see Cancer Genome Analysis Guide) |
| 4 | Presence in gene lists | Indicates if gene is listed in NHS National Genomic Test Directory (NGTD) and/or Cancer Gene Census. For NGTD, will also list Clinical Indications that match the patient's clinical indication group. |
| 5 | Ensembl Canonical Transcript ID | Ensembl Transcript ID for canonical transcript. |
| 6 | Impacted transcript region | The region of the transcript that is impacted by this CNV. |
| 7 | Alternative transcripts | Expandable table showing alternative (non-canonical) transcripts |
Resources¶
This section includes link outs to resources which may be useful for somatic copy number variant interpretation.
Info
Due to the nature of the resource and/or licensing constraints, we are only able to link out to the default home page for the above resources.