Variant Details Germline 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 | View in IGV | Click this to open the variant in IGV. |
| 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 | Genotype | The genotype assigned in germline variant calling e.g., heterozygous alt (0/1) or homozygous alt (1/1). |
| 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 germline. 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 e.g. Oncogene, Tumor suppressor, Ambiguous or Unknown.
- Tier as assigned by the Genomics England pipeline (see Cancer Genome Analysis Guide).
- The HGVS 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 (Oncogene, Tumor Suppressor gene, Ambiguous). |
| 3 | Tier | Tier as assigned by the Genomics England pipeline (see Cancer Genome Analysis Guide ). |
| 4 | Resource Linkouts | Linkouts to view entries releated to the gene in other resources e.g., "My Cancer Genome" database. |
| 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. |
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¶
Shows the population germline allele frequency obeserved in gnomAD exomes and internal Genomics England dataset.
Tip
By default the overall gnomAD exomes frequency is displayed, but 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 data, visit the gnomAD website.
Classification databases¶
Lists any matching entries in ClinVar, along with the interpretation, review status and number of submissions.
Warning
NOTE that this data is taken from a snapshot of ClinVar. The year and month (YYYY-MM) the ClinVar snapshot was taken is shown at the top of the section.
Tip
To view the latest ClinVar data, click the 'View in ClinVar' button to link out to the variant page on the ClinVar website in a new tab.
QC Flags¶
Description of the possible QC flags for germline small variants:
| QC Flag | Description |
|---|---|
| T | the variant is in the final 10% of the coding region and the impact of protein truncation regarding pathogenicity should be evaluated |