Reporting¶
The reporting page provides:
- A summary of variants - variants to report, reviewed variants, excluded variants
- Ability to add and view a case interpretation comment and comment history
- Summary of patient and clinical information for the case
- Summary 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.
Variants requiring interpretation¶
This card keeps a count of the number of Tiered variants requiring interpretation. At the top is a count of the total number of Tiered variants requiring interpretation (SNVs = Tier 1 and Tier 2, CNVs = Tier A and Tier B). A variant is classed as having been interpreted when it has been either excluded or had a classification value added.
Once the bar for each variant type is filled, and the message All Tiered variants are interpreted is visible, this means that all Tiered variants requiring interpretation have been attended to.
Variant tables¶
This card displays tables for both SNVs and CNVs which have been either added to the report, excluded, or that have had selections made by the user. When the case is closed, all actions in the variant tables are disabled.
Variants to report¶
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.
Key
| # | Section | Description |
|---|---|---|
| 1 | Variants to report | Displays all variants that have been added to the report after classification. There are two tables in this section, one for SNVs and one for CNVs |
| 2 | Actions (SNV) | Displays the classification for the SNV, and actions including 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 |
| 3 | Classification. | Displays the classification selected by the user, Excluded if the variant has been excluded, or a '-' if no classification has been selected |
| 4 | Variant (SNV) | The VCF format of the SNV |
| 5 | Gene (SNV) | HGNC gene symbol for the gene associated with the selected transcript. If no transcript has been selected, then No transcript selected is displayed, to remind you that a transcript needs to be selected. The gene pill is coloured green when the gene is green in at least one PanelApp panel of the most recent version at the time of case ingestion. |
| 6 | CDS / Protein change (SNV) | Contains the c. and p. HGVS nomenclature for the selected transcript. If no transcript has been selected, then No transcript selected 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. |
| 7 | Zygosity (SNV) | Relationship between the alleles at the locus |
| 8 | Contribution to phenotype (SNV) | The contribution to phenotype that has been selected for the SNV. The options for selection are Full, Partial, None, Unknown. If no option has been selected, then a '-' is displayed. |
| 9 | Variant drop-down | This can be expanded to display the latest selections for each input type from the interpretation history for the variant. In the Variants to report and Other reviewed variants tables this is the classification selection history. In the Excluded variants table this is the exclusion selection history. |
| 10 | Actions (CNV) | Displays the classification for the CNV. The Remove from report button moves the variant down into the Other reviewed variants table. When the case is closed, this button is disabled |
| 11 | CNV Genomic region / Cytoband (CNV) | The genomic region and cytoband of the CNV |
| 12 | Gene (CNV) | HGNC gene symbol(s) which the CNV affects. We show the first overlapped gene (additional genes are indicated wi/th a "+n" pill, with n being the number of genes) |
| 13 | Size (bp) (CNV) | Length of the copy number variant in base pairs |
| 14 | Type / Copy number (CNV) | The type of the copy number variant. Loss (deletion CNV) or Gain (duplication CNV). The copy number state is indicated by the number in brackets next to the type |
| 15 | Contribution to phenotype (CNV) | The contribution to phenotype that has been selected for the CNV. The options for selection are Full, Partial, None and Unknown. If no option has been selected, then a '-' is displayed. |
| 16 | Validation (CNV) | Validation requirements / validation results for the CNV |
Excluded variants¶
The Excluded variants table contains any variant that has specifically been excluded during classification. 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. Any excluded variants will not be included in the Summary of Findings.
The Excluded variants tables incorporate a subset of columns from the Variants to report tables, and a Reasons for exclusion column which contains any Reasons for exclusion checked by the user on the classification drawer when excluding the variant.
For a full history of exclusion selections, the drop-down can be expanded.
Other reviewed variants¶
The Other reviewed variants tables contains any variant that has been reviewed (i.e. has had selections made in the classification panel), but has not specifically been marked to add to the report or excluded. The columns in these tables tables correspond to those in the Variants to report tables.
Clicking on the Add to report button in the Actions column moves the variant up into the Variants to report table. 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 using the classification drawer.
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.
Patient information¶
As in the case summary, there is an equivalent section in the reporting page detailing patient details for the case. See the patient info section in the case summary page for further details.
PID
Non-NHS users are only able to view minimal patient information; patient sex, patient ID and Clinical Indication. Patient name, date of birth and NHS number are only visible to NHS users.
Family information¶
As in the case summary, there is an equivalent section in the reporting page family information for the case. See the family info section in the case summary page for further details.
Clinical information¶
As in the case summary, there is an equivalent section in the reporting page detailing clinical information for the case. See the clinical info section in the case summary page for further details.
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 on specific fields.
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 |