Closing a case¶
Cases can be closed by visiting the reporting page. Clicking on the Close case button in the top right of the reporting page will open an overlay which can be used to close the case. Before closing the case, please ensure that no PID has been entered whilst analysing the case. Providing an answer to the question Did the reported results explain the patient's phenotype? is mandatory in order to close the case; this information is required for populating the Summary of Findings PDF report and for creating Variant Interpretation Logs to populate CVA.
Once the confirm closure button is selected, the New IB case status will be updated to Closed, and a Case closed overlay will be displayed confirming successful closure of the case. Clicking on Interpretation Portal will navigate back to the Interpretation Portal in a new tab. At this point it will no longer be possible to make any kind of changes to the case. For information on how to reopen a case, please refer to the reopening a case section.
Key
| # | Section | Description |
|---|---|---|
| 1 | Close case button | Clicking this button opens the case closure overlay |
| 2 | Case closure question | Selecting an answer to whether the reported results explain the patient's phenotype is mandatory, as this is used to populate the Summary of Findings and CVA |
| 3 | PID warning | It is important to ensure no PID has been entered whilst analysing the case |
| 4 | Confirm closure button | When clicked, and given the case closure question has been answered, then the case will be closed and the case and outcomes will be added to CVA and the Summary of Findings will become available in the Interpretation Portal |
When the case has been closed, a banner will appear across the top of every page for the case indicating that the case has been closed.
Closed Cases¶
When a case is closed, the following banner will be displayed on the top of each page:
Whilst a case is in closed state, it is not possible to make any kind of changes to the case. In order to do this, the case will need to be reopened. This can be done in the same way as updating the case status, as per the guidance in the case status page.
For details on what happens to the case in the other systems when it is closed in the New IB, and vice versa, please visit the IP integration page.
Reopening a case¶
To reopen a case, follow the instructions in the reopening a case section on the changing case status page.
Abbreviations
| Abbreviation | Definition |
|---|---|
| ACGS | Association for Clinical Genomic Science |
| ACMG | American College of Medical Genetics and Genomics |
| CDS | Coding DNA Sequence |
| CNV | Copy Number Variant |
| CVA | Clinical Variant Ark |
| New IB | New Interpretation Browser |
| GEL | Genomics England |
| GMS | Genomic Medicine Service |
| GLH | Genomic Laboratory Hub |
| HGVS | Human Genome Variation Society |
| HTML | Hyper Text Markup Language |
| HSCN | Health and Social Care Network (N3) |
| IGV | Integrative Genomics Viewer |
| IP | Interpretation Portal |
| NGIS | National Genomics Informatics System |
| PID | Patient Identifiable Data |
| QC | Quality Control |
| SO | Sequence Ontology |
| SNV | Single Nucleotide Variant |
| SV | Structural Variant |
| TOMS | Test Order Management Service |
| UAT | User Acceptance Testing |
| VCF | Variant Call Format File |
| WGS | Whole Genome Sequencing |