Variant Details Somatic CNV¶
To open the variant details page, click the 'View details' button on your chosen variant in the variant list.
Variant and Quality Information¶
This panel allows you to view variant and quality information including:
- Variant coordinates and quality metrics.
- Link out to view the variant in IGV.
- Link outs to variant entries in external databases and resources.
Key
| # | Section | Description |
|---|---|---|
| 1 | GRCh38 coordinates | The chromosome and position for each breakpoint of the variant. |
| 2 | View in IGV | View this region in IGV. |
| 3 | Chromosomal bands | The chromosomal band(s) overlapping this variant. |
| 4 | Variant type | Variant type for this CNV: Gain, Loss or copy neutral loss of heterozygosity (LOH). |
| 5 | 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 is based on the quality score assigned by the variant caller (Canvas). For Dragen calls, "High" and "Low" indicate high and low confidence variants corresponding to PASS variants and all other variants, respectively. |
| 6 | Size (KB) | Size of the CNV in kilobases. |
| 7 | Copy number | Copy number for this CNV. |
| 8 | Resource Linkouts | Utilise these links to open the variant in other resources and databases e.g., Varsome. Clicking on the Varsome link out will open the variant in Varsome, with the "annotation-mode" set to somatic. Some copy number variants may be too large to analyse in Varsome. Clicking on the Decipher link out will open the Decipher gene track within the genomic region specified by the variant GRCh38 coordinates. |
Interpretation¶
This panel allows you to add interpretations to a variant, including:
- Flag a variant e.g., for further investigation.
- Classify according to the relevant guidelines.
- Comments.
- 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, Ambiguous or Unknown.
- 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).
- Link outs to gene entries in external databases and resources.
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 of the affected gene. |
| 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 | Resource Linkouts | Linkouts to view entries releated to the gene in other resources e.g., "My Cancer Genome" database. |
| 6 | Ensembl Canonical Transcript ID | Ensembl Transcript ID for canonical transcript. |
| 7 | Impacted transcript region | The region of the transcript that is impacted by this CNV. |
| 8 | Alternative transcripts | Expandable table showing alternative (non-canonical) transcripts. |
Resource Linkouts
Clicking on the "My Cancer Genome" database link out will perform a search for the gene in the "Biomarkers" section of the database.
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.