Curate Variant page
The Curate Variant page presents the most relevant variant information.
Components of the Curate Variant page
Top bar
that lists:
Gene symbol. When clicked, the software directs you to Curate Genes.
HGVS descriptions for genomic DNA, coding DNA, and protein-level changes
Variant effect
You can change Pathogenicity by selecting a different option from the dropdown menu.
Interpretation card
that features:
The Curated tab intended to be used for your curated variant interpretation. This text can be reused in the Variant Interpretation notes within a case
The Note tab for your draft notes on the variant
To edit your notes, select the tab (Curated or Note), and press the Edit button. Edit the text and apply the formatting. Don't forget to click Save!
Gene's related diseases card
that includes:
The number of gene-associated diseases as reported in OMIM, ORPHANET, CGD, ClinVar, and academic papers included in the Emedgene knowledge graph
The currently selected condition
Links to data sources
Inheritance mode icons where available
A Change button that opens the disease selection menu
Variant information card
that highlights:
The type of variant
Main effect relevant to the selected transcript
Gene symbol
HGVS format for coding and protein levels changes
You may select a different reference transcript from the dropdown menu.
To copy the HGVS descriptions in the clipboard, click the copy icon on the right.
ACMG Classification card
The ACMG Classification system in Emedgene supports a streamlined and flexible workflow across Analyze and Curate, allowing users to apply, manage, and reuse ACMG evaluations more effectively. Whether you're annotating a new variant or updating existing records, the tools available help maintain traceable and consistent variant interpretations.
Storing and managing ACMG classifications in Curate
You can store ACMG classification tags within Curate, enabling automated or manual application of ACMG logic to variants. This supports both new Curate entries and updates to existing ones.
Stored ACMG tags in Curate include classification logic, tag strength, tag-specific notes, and scores.
ACMG tags in Curate can be edited by users with the appropriate role and viewed (but not changed) by other users.
Whenever tags are added or modified, the system automatically recalculates the overall pathogenicity classification and score.
All changes to ACMG tags—including activation/inactivation, tag strength adjustments, and classification updates—are logged under Activities > Curate ACMG.
Changes to ACMG notes are not recorded in the activity log.
How stored classifications are applied in Analyze
When analyzing a case that contains variants with ACMG tags stored in Curate:
The existing ACMG classification is automatically applied to variants tagged by AI Shortlist.
This includes consideration of tag status (positive/negative), questions answered (yes/no), tag strength, and any associated notes.
These classifications are clearly marked as coming from Curate.
Updating ACMG data from Analyze
While reviewing a variant in Analyze, you have multiple options to interact with Curate through Curate actions.
Depending on whether the variant exists in Curate and your user permissions, the Curate button offers:
Add to Curate: For new variants not yet in Curate
Update in Curate: For existing variants. Updates include:
Pathogenicity classification
Variant interpretation
Associated gene-disease connection (unless custom)
Selected transcript (unless custom)
ACMG classification details (tags, score, strength, and notes)
Open in Curate: To view the stored Curate entry (available in previous versions as well).
This functionality ensures variant data stays synchronized across Curate and Analyze without manual duplication.
ACMG schema version warnings
When working in Curate, Emedgene keeps track of the ACMG schema version used for each curated SNV. If the variant was curated using an older schema than the one currently active in Analyze, you’ll see a warning in the ACMG Classification card.
Using an outdated schema may mean your classification is missing updated logic, revised strength definitions, or newly excluded tags.
Enhanced activity logging
To improve traceability:
Any update to a Curate entry via Analyze is reflected in the Activity Log, capturing the full history of changes.
Changes related to ACMG classification are grouped under a dedicated Curate ACMG category.
Related Cases card
that shows, for every case within your organization containing the tagged variant of interest:
Case name and genomic reference
CNVs: Variant details (genomic coordinates and size)
CNVs: Dynamic annotation overlap percentage filter
CNVs: Annotation overlap
Previously assigned pathogenicity
Case creation date
Previously assigned variant tag
Variant inheritance
Link to the case
For CNVs, all overlapping variants are displayed in the table. The minimal annotation overlap percentage filter is initially set to 70%, but it can be adjusted manually (1-100%).
Network Summary card
that shows, for each occurrence of the variant in each Curate database maintained by collaborators within your Network:
Collaborator
CNVs: Variant details (genomic coordinates and size)
CNVs: Dynamic annotation overlap percentage filter
CNVs: Annotation overlap
Case creation date
SNVs: Transcript
Gene-related disease
Variant Interpretation in the dropdown
For CNVs, all overlapping variants are displayed in the table. The minimal annotation overlap percentage filter is initially set to 70%, but it can be adjusted manually (1-100%).
Variants displayed in your Curate Variants table, which only have a Network Summary tab on the Variant page, are previewed from your collaborator(s)' Curate database(s) and are not part of your Curate database. To add such a variant to your Curate, click the Import button. Once added, you're free to edit Pathogenicity, Interpretation notes, Gene's Related Diseases, and Variant Transcript to your preference.
Activities panel
The Activities panel records a history of user activities on the Curate Variant page. Click the Activities button to open it.
Maximize button
The arrow icon on the top left of the Curate Variant page is a button that switches the view mode between:
Curate Variant table is hidden, while the Curate Variant page is maximized
Curate Variant table is shown, while the Curate Variant page is reduced
Last updated
Was this helpful?