Variant Annotations¶
Cases are processed via the bioinformatics pipeline and annotations are added by CellBase. Once a case arrives to the New Interpretation Browser (New IB), additional annotations are added from resources that are currently unavailable in CellBase.
| Annotation | Description | Source |
|---|---|---|
| gnomAD population frequency | Population germline allele frequency database | CellBase |
| Ensembl | Transcript and Protein ID annotations (ID, flags, consequences) | CellBase |
| ClinVar submissions | ClinVar Germline Database | CellBase |
| NGTD | NHS resource | Input by the clinician when ordering the test |
| PanelApp panels | GMS PanelApp | PanelApp |
| GEL population frequency | Internal germline allele frequency database | GEL dataset |
| Genes | Gene name and gene ID annotations for overlapping genes | CellBase |
| Coding sequence and protein change | Coding sequence and protein change | CellBase |
| Prioritisation results | Tier / segregation / mode of inheritance / penetrance | Genomics England Rare Disease Tiering, GEL Rare Disease pipeline |
GnomAD population frequency¶
The Genome Aggregation Database (gnomAD) is a population frequency database of large-scale sequencing projects from healthy cohorts.
- CellBase annotates whether a variant is present in gnomAD (exomes, genomes and mitochondrial datasets)
- The New IB displays the total population germline allele frequency as well as the subpopulations
Ensembl¶
Ensembl is a genome browser that provides gene annotations.
- CellBase annotates each variant with a transcript and protein ID from Ensembl.
- The New IB displays these annotations in the variant list and variant details page.
- The database version of Ensembl used by CellBase may not always be the most recent. Please see the latest version of the Rare Disease Genome Analysis guide and CellBase for further details.
ClinVar submissions¶
ClinVar is a public database of variant and phenotype relationships alongside supporting evidence and clinical interpretation histories.
- CellBase annotates whether a variant is present in Clinvar.
- The New IB displays the ClinVar ID, interpretation, review status and number of entries alongside a link to the ClinVar record in the variant list and variant details page for germline variants.
- The database version of ClinVar used by CellBase is displayed in the New IB and may not always be the most recent. Please see the latest version of the Camcer Genome Analysis guide and CellBase for further details.
National Genomic Test Directory¶
The NGTD for rare disease specifies which genomic tests are commissioned by the NHS in England, the technology by which they are available, and the patients who will be eligible to access to a test.
PanelApp¶
The GEL PanelApp knowledgebase allows virtual gene panels related to human disorders to be created, stored and queried and is used as the platform for achieving consensus on gene panels in the NHS Genomic Medicine Service (GMS).
- The Ensembl gene ID of each variant is used to match the variant to Panels in PanelApp
- The Panels in which the affected gene is present are then shown on the variant list and variant details page
GEL population frequency¶
This is a GEL internal population frequency dataset. Further details can be found in the Rare Disease Genome Analysis Guide.