Variant Details Somatic Small¶
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 population frequencies and COSMIC
- 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 can view variant coordinates and quality metrics, and link out to view the variant in IGV.
Key
| # | Section | Description |
|---|---|---|
| 1 | GRCh38 coordinates | The chromosome and position of the variant. |
| 2 | Ref > alt allele | Ref and alt alleles. |
| 3 | Variant allele frequency (VAF) | Proportion of total reads that support the variant allele. Calculated as alt/(alt + ref) |
| 4 | Alt allele/total read depth | Number of reads supporting alt allele and total total number of reads. |
| 5 | VCF Filter | Shows whether the variant has passed the variant caller filters. For variants that haven’t passed, the reason is shown in red e.g. ‘LowDepth’ Tumor or normal sample read depth at this locus is below 2. |
| 6 | QC Flags | Flags that indicate a variant call may be of a lower quality and at greater risk of being a false positive. Hover over the QC flag for a description. See QC flags tab for more information. |
| 7 | View in IGV | Click this to open the variant 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 genes and transcripts that overlap 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).
- The HGVS CDS and predicted protein change and consequence for each transcript.
Transcripts
By default, the canonical transcript is shown. But additional transcripts can be viewed by clicking 'Show alternative transcripts'.
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 | Transcript ID | Ensembl Transcript ID. |
| 6 | CDS Change | Coding sequence change (HGVS). |
| 7 | Protein ID | Ensembl Protein ID. |
| 8 | Protein change | Predicted protein change (HGVS) |
| 9 | Predicted consequence | Predicted consequences (SO terms) e.g. Missense variant |
| 10 | Alternative transcripts | Expandable table showing alternative (non-canonical) transcripts |
Population Frequencies¶
This panel displays the population germline allele frequency obeserved in gnomAD and internal Genomics England dataset.
Tip
By default the overall gnomAD frequency is displayed. Subpopulations can be viewed by clicking 'Show subpopulations'.
Warning
NOTE that this data is taken from a snapshot of gnomAD. The gnomAD version the snapshot was taken from is shown at the top of the section (e.g. 2.0.1). To view the latest gnomAD data, visit the gnomAD website.
Somatic Databases¶
This panel lists any matching entries in COSMIC, along with the number of samples.
Tip
Click 'Show tissue distribution' to view the sample counts by tissue. To view the latest COSMIC data, click the 'View in COSMIC' button to link out to the variant page on the COSMIC website in a new tab.
Warning
NOTE that this data is taken from a snapshot of COSMIC. The COSMIC version the snapshot was taken from is shown at the top of the section (e.g. v89).
This panel lists any matching entries in the Cancer Hotspots database, along with the number of samples and the tissue sample distribution. A match is defined as any variant affecting the same amino acid residue, irrespective of the resultant amino acid change. Please see here prior to using these annotations towards variant interpretation.
Tip
Click 'Show sample distribution' to view the sample counts by tissue. To view the record in Cancer Hotspots, click the 'View in Cancer Hotspots' button to link out to the variant page on the Cancer Hotspots website in a new tab.
Info
Cancer hotspot annotations are not currently available for splice variants or InDels, but will be in a future release. Until then, we recommend you check the cancerhotspots.org website for these variants.
QC Flags¶
Description of the possible QC flags for somatic small variants:
| QC Flag | Description |
|---|---|
| GE | a structural variant with at least one breakpoint with a population germline allele frequency over 1% in either GESG or GECG datasets, internal Genomics England germline variant datasets used as panels of normals (indicates potential un-subtracted germline variants). For further details please refer to Cancer Genome Analysis Guide |
Resources¶
This section includes link outs to resources which may be useful for somatic small 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.