Variant Details Somatic Small¶
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 of the variant. |
| 2 | Ref > alt allele | Reference and alternate 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. |
| 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. |
| 8 | Origin | Indication of the variant’s origin as specified by TINC e.g. Somatic or Uncertain. This value will only be shown for cases that have gone through the TINC workflow. |
| 9 | 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. Clicking on the SpliceAI link out will open the variant in SpliceAI with default settings applied. 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 genes and transcripts that overlap this variant.
It includes:
- Mode of action as listed in Cancer Gene Census i.e., 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.
- The HGVS coding sequence (CDS) and predicted protein change and consequence for each transcript.
- 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'.
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 i.e., Oncogene, Tumor Suppressor gene, Ambiguous or Unknown. |
| 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 | Transcript ID | Ensembl Transcript ID. |
| 7 | CDS Change | Coding sequence change (HGVS). |
| 8 | Protein ID | Ensembl Protein ID. |
| 9 | Protein change | Predicted protein change (HGVS). |
| 10 | Predicted consequence | Predicted consequences (SO terms) e.g. Missense variant. |
| 11 | 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.
Population Frequencies¶
This panel displays the population germline allele frequency obeserved in gnomAD exomes and internal Genomics England dataset.
Tip
By default the overall gnomAD exomes frequency is displayed. Subpopulations can be viewed by clicking 'Show subpopulations'.
Warning
NOTE that this data is taken from a snapshot of gnomAD exomes. 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 exomes 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.