Classified Variant Database (Opal Clinical)

Jeanette McCarthy -

The Classified Variant Database allows all workspace users to browse all variants that have been classified or are in the scoring process in the workspace. Each entry in the Classified Variants Table represents a unique scoring session and variant classification. User can review the Scoring Sheet, Variant History, Citations and Report History for a scoring session/variant classification in the Variant Information Tab. Lab Directors can monitor the classification of variants in the workspace and Manage Variants by retiring outdated or incorrect classifications. A Filters Menu menu to the left of the table provides tools to filter the entries by various metrics.


You can reach the Classified Variant Database page from:
-  Opal Home page  >>Classified Variant Database link
-  Opal Toolbar  >>  Menu dropdown >>Classified Variant Database option


Classified Variants Table

All columns of the Classified Variants table are sortable by clicking on the column header. Hovering over an entry in the table will shows the Variant Information Tab header. Open the tab by clicking on the tab header.

Click the checkbox to the left of an entry to select or unselect it. To select or unselect all variants visible on the current page click on the checkbox in the table header.
Not sortable.
The official HGNC (Hugo Gene Nomenclature Committee) symbol for the gene.
Nucleotide Change
The HGVS (Human Genome Variation Society) notation for the nucleotide change for the representative transcript.
Protein Change
The HGVS (Human Genome Variation Society) notation for the protein change (if any) for the representative transcript.
The condition the variant was scored and classified for.
The inheritance mode of the condition-gene-association used for this scoring session.
The classification set for this scoring session.
Scoring Status
The current status of the scoring session. Possible values are Scoring, Scored and Classified.
Scoring Started Date
The date the scoring session was started.
Scoring Started By
The user who started the scoring session.
Scoring Approved Date
The date the clinical report containing this scoring session was approved.
Scoring Approved By
The Lab Director who approved the clinical report containing this scoring session.
Retirement Status
The retirement status of a scoring session/classification can be either Active or Retired.
The variant classification is visible in Report History in the Score Variant tab of a clinical report and can be accepted or selected as starting point for a new scoring session.
The variant classification is not visible in Report History in the Score Variant tab of a clinical report.
Only a Lab Director can change the retirement status by selecting one or more table entries and clicking on Manage Variants.
Last Confirmation Status
If the variant was submitted for confirmation for any of the clinical reports using this scoring session/classification the last updated Confirmation Status is displayed.
Report History
The number of clinical reports using this scoring session/classification. Click on the hyperlink to open the Report History in the Variant Information Tab.

Manage Variants

Lab Directors can manage which scoring sessions/variant classifications are visible in Report History in the Score Variant tab by setting the Retirement Status to either Active or Retired. To change the Retirement Status select one or more scoring sessions/variant classifications and click the Manage Variants button. In the Manage Variants dialog box select the desired Retirement Status and click on Apply to save the changes.

The Manage Variants button is only available to user with Lab Director permissions. 

Variant Information Tab

The Variant Information tab displays more details about the scoring session/variant classification.

The Summary tab displays the Variant Description, a user generated text, and the Scoring Summary from the scoring session, an Opal generated text based on the answers to the ACMG scoring criteria.
Variant History
The Variant History tab lists all user actions during the scoring session in chronologically descending order, providing the user name, date and action performed.
The Citations tab contains all citations that were curated for this scoring session. The citations are grouped into Cosegregation Studies, Functional Studies and General Studies.
Report History
The Report History lists all clinical reports that use this scoring session/variant classification. The information provided for each clinical report include Zygosity, Confirmation Status, Report Section, Test (Indication), HPO Terms, Report Status, Report Date and Report [Accession].
Clicking on the report Id hyper link opens the clinical report in a new browser tab.
Alternate Transcripts
This tab list all alternative transcripts for the gene in the Transcipts-Proteins-Consequences table and the Consensus CDS and RefSeq HGVS table. In both tables the Canonical Transcript is highlighted.

Filters Menu

The filters menu 

Gene Symbol
Enter one or more official HGNC gene symbols to filter the classified variant by. This search field is not case sensitive.
Choose a workspace panel to filter for scoring sessions/classified variants within the panel genes.
Display variant scoring sessions with the selected classification. The dropdown menu will include the standard classifications, any custom classifications defined in this workspace and the option No Class to filter for variant scoring sessions with no classification. 
Scoring Status
Select to show only scoring sessions with the status Scoring, Classified or Scored.
Scoring Started By
This dropdown menu allows you to filter the scoring sessions by the user who started the scoring session.
Scoring Started Date
Filter based on the date variant scoring sessions were started. 
Scoring Approved By
This dropdown menu allows you to filter the scoring sessions by the user who approved the Clinical Report and all scoring sessions created within the report.
Scoring Approved Date
Filter based on the date variant scoring sessions were approved. Variant scoring sessions are approved when the Clinical Report is approved.
Retirement Status
Select to show only scoring sessions with the status Retired, Not Retired or All
Last Confirmation Status
Display variant scoring sessions with the selected Confirmation Status. If a variant has multiple scoring sessions, the Confirmation Status from the newest (last) scoring session is used.
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