What's New
The Variant Curation Interface (VCI) introduces two major changes to how you classify variants in Franklin:
Guided, structured classification - instead of managing ACMG rules in a flat list, VCI walks you through each criterion, organized into sections. You can document your reasoning at every step with curator notes, and the system tracks a running Suggested Classification as you go.
Per-condition classification - variants can now be classified independently for multiple conditions. Each condition has its own rules curation, curator notes, and classification status.
VCI is available for germline SNV/indel variants in Cases and in the Knowledge Base.
Classifying a variant
Step 0: Opening the VCI
You can access the VCI from two places:
Workbench/Variants page - Click the classification flag button on any variant tile.
Variant pop-up - Click the "Classify Variant" button.
Step 1: Select a Condition
At the top of the VCI, use the Condition dropdown to select the condition you are classifying for.
The dropdown is organized into three categories:
Curated - Conditions curated in your organization's gene curation app
Gene Associated - Conditions associated with the gene in external resources
All Conditions - All other conditions, including search results and free-text entries
Step 2: Curate ACMG Rules by Section
To select and apply specific rules, press the "Choose rules", it will take you to the ACMG Rules tab, where all applicable criteria are organized into sections (e.g., Population Data, Computational Evidence, Functional Data, etc.). The section order is fixed and based on rule severity.
Rule Color Coding
Color | Meaning |
🔴 Red | Met & Pathogenic rule |
🟢 Green | Met & Benign rule |
⬜ Gray | Unmet rule |
White | N/A |
Drilling into a Section
Click on any section to open the Section Curation page. Here you can:
Set Met Criteria: Met / Unmet / N/A
Set Strength:
Pathogenic rules: No Influence / Supporting / Moderate / Strong / Very Strong / Stand Alone
Benign rules: No Influence / Supporting / Strong / Stand Alone
Add a Curator Note (rich text) - documents your reasoning for this section's criteria
Add an Interpretation text (rich text) - the same field that appears in the summary tab and in patient reports
When you save a section, the Suggested Classification updates immediately, and a section status indicator appears showing who saved it and when.
Step 3: Finalize the Classification
Click "Summarize & Classify" from the ACMG Rules tab to go to the Variant Interpretation summary tab.
Franklin calculates a Suggested Classification in real time based on your met/unmet rules - the same algorithm as the Franklin ACMG Classification tab. It updates as you curate and is visible throughout the VCI.
Curator Notes Summary
This field consolidates all curator notes from your sections, with each section's name as a bold header.
Editing: You can freely edit this field. Once edited, it will no longer auto-sync with individual section notes - a banner will notify you: "Changes will not be applied to the section's curator note and vice versa."
Refreshing: Click the Refresh button to restore the consolidated view. The button is disabled when the field is already in sync.
Interpretation Text
The Interpretation field is shared across all section pages and the summary tab, edits anywhere are reflected everywhere.
Saving the Classification
Action | What it does |
Save Draft | Saves your work in progress; available until a Final classification exists in the case |
Save Final | Submits the final classification; once saved, Save Draft is disabled for this case |
Tips & Best Practices
Work section by section. Save as you go - the Suggested Classification updates incrementally, giving you a running view of where the evidence is pointing.
Use Curator Notes at the section level to capture the reasoning behind each group of criteria. They automatically consolidate into the Curator Notes Summary at the end.
Use Interpretation Text for the narrative that will appear in the patient report - it's editable in both section pages and the summary tab.
Select the right condition before you start. All rules, notes, and statuses are stored per condition.
Use the full-screen view for complex variants where you need more space.