Recording Interpretation (SNVs)

Disclaimer

The clinical interpretation of referrals and variants should follow your local best practice guidelines.

There are a number of features designed to aid in case and variant interpretation, and tracking those interpretations. SNV interpretation can be performed on the variant grid, or the variant details page, using the classification panel. This panel provides the ability for variants to be commented on, a contribution to phenotype and transcript selected, and ACMG criteria and a classification to be added. A history of any comments and classification can be seen in the History panel below the classification panel, along with information on who provided the interpretation and when.

Any variant with an interpretation history, which has not been added to the report, will be visible by default in the Other reviewed variants table on the reporting page.

Classification and Exclusion

A variant can be classified or excluded using the Classification drawer on the variant grid or the Classification panel in the variant details page.

All fields and buttons are disabled when the case is closed.

It is recommended that once classification of a variant is complete, the tooltip is used to manually check and verify that the points and codes assigned, and the points total, are correct.

ExclusionTranscript selectionContribution to phenotypeVariant commentAdd criteria and classifyAdd to report

Exclusion

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.

A variant can be excluded by clicking the Exclude variant button in the Classification pane. This will update the classification at the top of the card to Excluded, hide the fields for classifying the variant, and reveal two new fields, to select one or multiple reasons for excluding the variant, and add an associated comment to record rationale (both optional fields). The Reasons for excluding selection options are: Incompatible phenotype, No relevant disease association, Inherited from unaffected parent, No higher than VUS, Artefact, Common, and Other. There is a maximum limit of 10,000 characters for comments. Selections can be removed by deselecting the selected check-box(es).

To unexclude the variant after exclusion, uncheck the checked Exclude variant box. This will set the classification drawer back to the default view.

Exclusion comments

Exclusion comments can be edited or removed by any user, by opening the menu next to the comment and clicking Edit or Delete. This allows for easy removal in the case of any accidentally included patient identifiable information (PID). When an exclusion comment is edited, the username and timestamp associated with the comment will update to that of the current user and the current time, and the comment will become the most recent comment (therefore the comment that is displayed at the top of the classification panel).

When an exclusion comment is deleted, the comment text will be replaced by Removed, and the comment displayed in the classification panel will either be cleared if there was no previous version of the comment, or it will revert to the previous version of the comment.

Transcript selection

If the variant has any associated gene(/s), a transcript selection can also be added alongside the classification. If it does not then this drop down will not be displayed for the variant.

Transcripts available in the drop down are grouped by gene, with a flag displayed next to the transcript to indicate whether it has the most severe consequence for the gene (S), and whether it is a Mane Select (M) or Mane Plus Clinical (M+) transcript. A transcript could have no flags if it does not produce the most severe consequence for the gene, it could have only one of S, M or M+, or it could have a combination of multiple of these. Currently the transcripts in the drop down are not ordered in any specific priority.

Selections can be reset using the drop down menu and selecting Reset selected transcript, and the drop down will then display Select.

Contribution to phenotype

A contribution to phenotype can also be added alongside the classification. The options provided are Full, Partial, None and Unknown.

Selections can be reset using the drop down menu and selecting Reset contribution to phenotype, and the drop down will then display Select.

Variant comment

Comments can be added using the Variant comment box in the Classification pane. Clicking Cancel will prevent the comment from being saved, and this can be checked in the History panel. See the history page for details on editing comments. There is a maximum limit of 1024 characters for comments. If you enter a URL, this will be recognised and loaded as a clickable hyperlink when saving the comment.

Comments can be edited or removed by any user, by opening the menu next to the comment and clicking Edit or Delete. This allows for easy removal in the case of any accidentally included patient identifiable information (PID).

When a variant comment is edited, the username and timestamp associated with the comment will update to that of the current user and the current time, and the comment will become the most recent comment (therefore the comment that is displayed at the top of the classification panel).

When a variant comment is deleted, the comment text will be replaced by Removed, and the comment displayed in the classification panel will either be cleared if there was no previous version of the comment, or it will revert to the previous version of the comment.

Classification

The classification is based on the ACMG/AMP 2015 framework, as adapted and clarified in the ACGS Best Practice Guidelines for Variant Classification in Rare Disease (2024).

The user can manually classify a variant as one of Benign, Likely benign, Uncertain significance, Likely pathogenic and Pathogenic. Alternatively, when ACMG criteria are added for the variant, the system will auto-calculate a classification based upon the points total from the added criteria. Headers are colour coded according to pathogenicity (Benign or Likely benign = green, Pathogenic or Likely pathogenic = pink, Uncertain significance = blue).

It is recommended that after adding ACMG criteria, the tooltip is used to manually check and verify that the points and codes assigned, and the points total, are correct.

ACMG criteriaAuto-calculated classificationClassification tooltipManual classification

ACMG criteria

ACMG criteria can be added by clicking the +Add button in the classification drawer. This opens up a selection panel, where Evidence code and Strength can be selected, and an associated Comment added. Evidence code and strength are mandatory, whilst comment is optional. The Evidence code selection box can be typed in to narrow the drop down options to the code(/s) of interest. Upon selecting a code, the system assigns a default strength, which can then be altered by using the drop-down should you wish.

Once the code has been added, it is displayed as a colour-coded tab underneath the Evidence header, which can be clicked on to reveal the strength assigned and any comment added. Clicking on the menu allows the code to be edited or removed. Editing allows the strength and comment to be amended, or the code to be changed entirely. Removing the code omits the code from the classification evidence for the variant - it will no longer be visible in the front end, but will remain in the back end systems and the History for audit trail purposes. Tabs for benign and likely benign codes are coloured green, and those for pathogenic and likely pathogenic codes are coloured pink.

Auto-calculated classification

As ACMG evidence codes are added to a variant, the system will auto-select a classification in the classification drop-down (indicated by the (calculated) suffix in the drop-down and history log). Additionally, the bar underneath the classification header will become active and will display a points marker, points total, and colour to reflect the total points across the assigned ACMG codes for the variant.

If evidence codes are added or removed, the assigned classfication will be re-calculated and auto-selected accordingly by the system, with points total, points marker and slider updating to reflect the new points total. The auto-selected classification can be manually overridden if required, using the classification drop-down (see Manual classification section). Addition of ACMG codes will override any manual classification selection.

Points ranges for the auto-calculated classification are as follows (Tavtigian et al., 2020):

Classification	Points
Pathogenic	≥ 10
Likely pathogenic	6 - 9
Uncertain significance	0 - 5
Likely benign	-1 - -6
Benign	≤ -7

The exception to the above behaviour in the case of assignment of BA1, which sits outside the point system and overrides all other codes. If this code is added, the points total will disappear, the points marker will move to the end of the Benign range, and the classification will be auto-calculated as Benign.

Classification tooltip

As ACMG codes are added, the points total can be verified by clicking the tooltip to the right of the classification at the top of the drawer. This will provide a break down of the scores attributed to each code, and the total score across all codes for the variant. It also provides a link-out to the ACGS guidelines (2024), where the codes and strengths were derived from.

The exceptions are:

• When BA1 has been added, the tooltip will not display any points values, as it sits outside the points system and overrides all other codes
• If a classification is selected manually, the tooltip will not be present as the classification has not been derived from the points total

Manual classification

A classification can be selected manually using the classification drop-down. This can also be used to override any system-calculated classification. A record will be saved in the history log, in the same way as for all other user selections. Prior classification(s) will remain visible in the history log.

When an auto-calculated classification is overriden, the points tooltip will disappear, and the points slider will be greyed out with any points total no longer visible.

If further ACMG codes are then added, the classifcation will be re-calculated by the system, and the manual classification overridden.

Reset classification

The classification can be reset using the classification drop-down, by selecting Reset classification, which will set the field back to the default Select status, and set the classificaiton at the top of the card back to None Selected.

Add to report

Variants can be added to the Variants to report table in the reporting page by clicking the Add to report button at the top of the classification drawer. Clicking the button again will then remove the variant from the report.

Pathogenic and Likely Pathogenic classifications

Variants with Pathogenic or Likely pathogenic classification selected can only be added to the report if all fields in the classification drawer have been completed. This is because the information is required in order to pass the variant to CVA. Any attempt to add the variant to the report by clicking the Add to report button without completing all fields will trigger an error message to indicate that those fields are required. Once those fields have been filled in, then the error messages will disappear and clicking the Add to report button will now successfully add the variant to the Variants to report table. The Add to report button will be replaced by a Remove from report button which can be used to remove the variant from the Variants to report table.

If the selection for any field is cleared after it has been added to the Variants to report table, then the variant will be automatically removed from the table and be moved into the Other reviewed variants table.

All other classifications

Variants with any other classification types or without a classification selected can be added to the report by clicking the Add to report button, with no mandatory fields required.

Excluded variants

Excluded variants are added to the Other reviewed variants table by default. Any attempt to add an excluded variant to the report will result in an error message.

Abbreviations

Abbreviation	Definition
ACGS	Association for Clinical Genomic Science
ACMG	American College of Medical Genetics and Genomics
CDS	Coding DNA Sequence
CIP-API	Genomics England Clinical Interpretation API
CNV	Copy Number Variant
CVA	Clinical Variant Ark
EQ	Exit Questionnaire
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
IB	Interpretation Browser
IP	Interpretation Portal
NGIS	National Genomics Informatics System
PID	Patient Identifiable Data
QC	Quality Control
SoF	Summary of Findings
SO	Sequence Ontology
SNV	Single Nucleotide Variant
SV	Structural Variant
TOMS	Test Order Management System
UAT	User Acceptance Testing
VCF	Variant Call Format File
VILs	Variant Interpretation Logs
WGS	Whole Genome Sequencing