Reporting¶
The reporting page provides a summary of variants (variants to report, reviewed variants, excluded variants), the case interpretation comment and any comment history, and a record of the software and dataset versions used to process and interpret the case. Cases can be closed from this page (case status can also be updated using the header drop-down, see the closing a case page for more details).
Case interpretation¶
Here, the overall case comment can be added, summarising your interpretation of the case (N.B. there is a 10,000 character limit). This is mandatory, as the information is collected to populate the Summary of Findings and CVA. The comment can be edited by any user after it has been written, using the menu button. It can also be deleted but only by the user who wrote the comment. Upon comment deletion, the case comment will be replaced by the previous edit version of the comment if one exists, otherwise it will revert to its default state and a new comment can be added.
Attempting to close the case without filling in this comment field will result in an error message and it will only be possible to close the case once the comment has been added.
Variant tables¶
The Variants to report table contains any variant that has specifically been marked to add to the report. Adding a variant to the report means it will be included in the Summary of Findings, so should include all reportable variants.
The Other reviewed variants table contains any variant that has been reviewed (i.e. made any selections for in the classification panel), but has not specifically been marked to add to the report. It also contains any variants that have been marked as excluded. Excluded variants are variants that have been determined to not require any further interpretation or classification for a specific reason, such as being an artefact or being too common.
Key
| # | Section | Description |
|---|---|---|
| 1 | Variants to report Actions | Actions including View details (navigates to the variant details page for the variant), and a Remove from report button which moves the variant down into the Other reviewed variants table. When the case is closed, this button is disabled |
| 2 | Variant | The VCF format of the variant |
| 3 | Gene | HGNC gene symbol for the gene associated with the selected transcript. If no transcript has been selected, then Select transcript is displayed, to remind you that a transcript needs to be selected. The gene is coloured green when it is green in the most recent PanelApp version, and that panel matches the GMS PanelApp panel applied to the patient (i.e. it is counterpart to the GMS version). |
| 4 | CDS / Protein change | Contains the c. and p. HGVS nomenclature for the selected transcript. If no transcript has been selected, then Select transcript is displayed, to remind you that a transcript needs to be selected. If the transcript does not result in a CDS / Protein change, then '-' are displayed. |
| 5 | Zygosity | Relationship between the alleles at the locus |
| 6 | Contribution to phenotype | The contribution to phenotype that has been selected for the variant. The options for selection are Full, Partial, None, Unknown. If no option has been selected, then a '-' is displayed. |
| 7 | Classification | Displays the classification selected by the user, Excluded if the variant has been excluded, or a '-' if no classification has been selected |
| 8 | Variant drop-down | This can be expanded to display the latest selections for each input type from the interpretation history (classification and exclusion history) for the variant |
| 9 | Other reviewed variants Actions | Actions including View details (navigates to the variant details page for the variant), and a Add to report button which moves the variant up into the Variants to report table. When the case is closed, this button is disabled. N.B. all fields are mandatory for Pathogenic and Likely Pathogenic classifications - if there are missing selections then an error will appear when clicking the Add to report button, and it will not be possible to add the variant to the Variants to report table until those selections have been made. |
Case interpretation history¶
Here, the full history of case comment and any edits that have been made to the case comment are visible. It is also possible to edit comments here using the menu next to the comment, and to delete the comment if it is your comment.
Software and dataset versions¶
As in the case summary, there is an equivalent section in the reporting page detailing the software and dataset versions used for the case. See the software and dataset section in the case summary page for further details.
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 |