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 interpretationVariant tablesCase interpretation historyPatient infoFamily infoClinical infoSoftware and dataset versions

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 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 Other reviewed variants table 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.

Key

#	Section	Description
1	Variants to report Actions	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
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 No transcript selected 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 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.
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 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.
9	Excluded variants	Displays all excluded variants. These cannot be directly added to the report from the reporting page - to do this you will need to click on Details, unexclude the variant, and add to the report. There are no mandatory fields for excluded variants.
10	Other reviewed variants Actions	Actions including 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.

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.

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