Frequently Asked Questions¶
Why does the Portal payload differ from the CIP-API?¶
Referral payloads downloaded from the Portal may look slightly different from those taken directly from the CIP-API.
This happens because the Portal retrieves data it has in memory for a case, which can be a mix of legacy and updated formats. Where there are differences, always trust the payload from the CIP-API.
What are tags?¶
Tags highlight issues that may affect analysis. They are managed by the CIP-API or bio-operations and flag things like missing variants in the DSS.
What are email notifications?¶
Daily emails alert GLHs to cases with status changes. Routine and urgent referrals are sent separately, each listing key details such as Referral ID, Status, Organizations, Clinical Indication, and Type.
To update recipients, submit a Service Desk ticket.
What do warnings and errors mean?¶
Not all warnings or errors indicate system problems.
- N/A under patient details means the Portal couldn’t connect to TOMS (expected when data is unavailable).
- Other messages indicate missing data from TOMS such as PID, notes, or consent.
In the Referral Grid, "Unable to retrieve patient data" also means a TOMS connection issue.
What are Interpretation Services?¶
These are tools/algorithms that prioritize variants to help find the cause of a patient’s condition. Each produces an Interpreted Genome.
The Rare Disease Interpretation Browser lets you review results and select primary findings.
For details on Tiering and Exomiser, see the Genome Analysis Guide v2.0.
Note: A score of 0 may hide a variant in Exomiser, but ranked results (1–3, score > 0.75) are still shown in the payload.
Why don’t I see Genomic and Data checks?¶
The WGS pipeline already checks reported vs. genetic sex before running. Because it always passes or fails at that step, the information was removed from the Referral page.
What are Decision Support Systems (DSS)?¶
DSS applications support case review, MDT discussions, and reporting. They also allow exploration beyond Interpretation Service outputs. See DSS-specific guides for details.
What is CVA?¶
The Clinical Variant Ark (CVA) is Genomics England’s knowledge base for comparing similar cases. It shows prioritized variants along with linked SoFs, Reported Outcomes, and Interpretation Logs.
Access: CVA Portal.
What is CellBase?¶
CellBase integrates biological data for annotation of genomic features. The Interpretation Browser uses it for extra variant annotations.
Why is my referral flagged?¶
Cases that fail QC checks are automatically flagged.
See the Referral Flags page for details on flag types and where they appear in the Portal.
Which Exomiser score is shown?¶
The Interpretation Browser shows the combined Exomiser score. The individual variant and phenotype scores are available in the payload.
Why don’t I see read depth for my variant?¶
Read depth is reported as provided by interpretation services:
- Homozygous reference variants show
-/-in the Interpretation Browser. - "N/A" means no depth was reported.
Depth may differ from IGV due to filtering. Exomiser and 100K VCF-added variants do not report depth.
How does the Exomiser filter work?¶
It’s a “greater than” filter. By default, only variants with a combined score > 0.75 are shown.
What are CVA classifications?¶
These summarize classifications from reporting outcomes questionnaires. They don’t include DSS-only classifications, which are stored in Variant Interpretation Logs (accessible via CVA).
What does shading in the Portal mean?¶
- Yellow referrals: draft work saved
- Green variants: added from VCF or called by Exomiser but not yet validated
How do I update a closed interpretation?¶
See the workflow guide: Updating a closed referral.