The Curate Variant Table is your central view of all variants stored in your organization’s Curate database. It provides quick access to variant details, pathogenicity, and search tools, with clear counts of curated records to make tracking easier.

The Curate Variant table features:

1. A Search bar where you can search for variants by gene symbol or genomic position

2. Gene column

3. Variant details column

4. Pathogenicity column

1. Search

• A search bar allows you to quickly find variants by:

  • Gene symbol (e.g., BRCA1)

  • Genomic position (e.g., chr17:43071077 A>G)

2. Column Overview

• Gene Column – Displays the gene(s) associated with each variant.

• Variant Details Column – Shows genomic coordinates and mutation information.

• Pathogenicity Column – Indicates the variant's classification (Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign).

All columns support alphabetical or numerical sorting where applicable for quick navigation.

Variant Counts

To improve clarity when browsing large databases, the Curate interface now shows real-time counts of curated records:

• If your organization has a network connection, count text will display both number of total filtered variants from your native Curate database and number of filtered variant interpretations from the connected network (if available).

• If your organization does not have a network connection, count text will display only number of curated variants from your native Curate database.

Note:🔻All the Curate Variant table columns allow for alphabetical sorting.

• If the variant is already in your Curate database, you will see an Open Curate button on the Variant page Top bar.

Curate Variant annotations allow you to see if a variant already exists in your Curate database, access its stored pathogenicity, and view related data across multiple sections of the Variant Page. This ensures consistent interpretation and faster decision-making.

How do I know if the variant is already in Curate?

The top bar of the Variant Page features a dropdown menu with three options:

• Open – Available if the variant already exists in your Curate database.

• Add – Available if the variant does not exist in Curate; use it to add the variant directly to Curate.

• Update – Available if the variant exists but has new notes, interpretation, or pathogenicity to sync.

Each option is enabled or disabled based on the variants' status in the Curate database.

Curate annotations are displayed across multiple locations in the Variant Page and Variant Table:

Where can I find Curate annotations?

1. > Known Variants > 👁️ Curate Pathogenicity badge

1. > > 👁️ Curate and CurateSV (make sure to tracks of interest)

The Curate Variants page consists of:

1. Curate Navigation panel (left),

2. Curate Variant table—lists your curated variants (center),

3. Curate Variant page—highlights the most clinically relevant variant information (right).

The Curate application in Emedgene lets you add and curate variants at the organization level, so they can be reused across cases and included in annotations during the case pipeline.

You can now delete variants directly from Curate without needing Emedgene support. Users with the appropriate permissions will see a Delete button on the Variant Page.

Deletion permanently removes the variant and its associated data from your organization’s Curate database, making it unavailable for future annotations. Network-only variants cannot be deleted locally. Once deleted, the action cannot be undone, though an audit log will record the deletion for traceability. Use this feature cautiously and confirm details before proceeding.

The Curate module allows you to store, organize, and manage variants for long-term reference and knowledge sharing across your organization. Variants can be added to Curate manually (single or batch) or exported directly from the Variant Page.

1. Add a new variant in Curate

To manually add a new variant:

1. Click on the button

2. Select a desired

3. Fill the variant's description in the format "chr1:123456 A>G"

4. Click Save. You will be directed to the variant's

2. Export from the Variant page

For customers using Emedgene Analyze, it is possible to export a variant from the Variant page directly to Curate:

1. the variant

2. Set

3. Click on the Export to Curate button on the . You will be directed to the variant's in a new browser tab

V37 and below: If the variant is already in your Curate database, you will see an Open Curate button. Otherwise, you will see an Export to Curate button.

V38+: Clicking on this button will open a menu with 3 options:

1. If the variant is not already in your Curate database, you will see an Add to Curate button. Clicking this button adds the variant to Curate for further review and editing.

2. If the variant is already in your Curate database, and you have the “kms_export” role, you will see an Update in Curate button. Clicking this button updates the variant record in Curate with information from the current Analyze session, including:

   1. Pathogenicity

3. Batch upload variants to Curate

The batch upload feature allows you to add large sets of variants at once via a validated CSV template.

1. Go to Curate and click Add New.

2. Switch to Batch Mode to enable bulk upload.

3. Download the sample CSV template provided.

4. Fill in variant details following the format in the template.

• Emedgene will automatically validate the file to ensure compatibility and accuracy.

• Once uploaded, a toaster notification (bottom-left) will confirm progress and report any errors.

• If you attempt to leave the page before the upload is complete, a message will appear stating that any unsaved changes will be lost.

Batch upload limits:

• Maximum 5,000 variants per upload or 10 MB file size.

• Multiple concurrent uploads are supported.

• If an upload fails or partially validates, you must start a new upload after correcting the error file.

The Curate Variant page presents the most clinically relevant variant information.

The Curate Variant page is comprised of:

Top bar

that lists:

1. Gene symbol. When clicked, the software directs you to

2. HGVS descriptions for genomic DNA, coding DNA, and protein-level changes

3. Variant effect

Interpretation card

that features:

1. The Curated tab intended to be used for your curated variant interpretation. This text can be reused in the within a case

2. The Note tab for your draft notes on the variant

Note: 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:

1. The number of gene-associated diseases as reported in OMIM, ORPHANET, CGD, ClinVar, and academic papers included in the Emedgene knowledge graph

2. The currently selected condition

3. Links to data sources

Variant information card

that highlights:

1. The Type of variant

2. Main Effect relevant to the selected transcript

3. Gene symbol

4. HGVS format for coding and protein levels changes

Note: You may select a different reference transcript from the dropdown menu.

Note: To copy the HGVS descriptions in the clipboard, click on 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.

How Stored ACMG Tags Work

• Stored ACMG tags in Curate include classification logic, tag strength, tag-specific notes, and scores

• These tags 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

_{Note: 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 those variants

• 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:

1. Curate Button 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

This functionality ensures variant data stays synchronized across Curate and Analyze without manual duplication.

1. Curate 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 section of the variant.

Using an outdated schema may mean your classification is missing updated logic, revised strength definitions, or newly excluded tags.

1. Enhanced Activity Logging

To improve traceability:

• Any update to a Curate entry via Analyze will now be reflected in the Activity Log, capturing the full history of changes

• Changes related to ACMG classification are grouped under a dedicated Curate ACMG category

Use Case Example

When evaluating a variant in Analyze:

1. Apply ACMG tags either manually or via auto-classification

2. Use the Update in Curate button to sync this evaluation into your Curate database

3. If the same variant is later reviewed in another case, the stored classification is automatically retrieved—saving time and maintaining consistency

This ACMG classification integration helps streamline your interpretation workflow, supports traceability, and ensures that your variant evaluations are consistently reused and refined across the platform.

Related Cases card

that shows, for every case within your organization containing the tagged variant of interest*:

1. Case name and genomic reference

2. CNVs: Variant Details (genomic coordinates and size)

3. CNVs: dynamic percentage filter

*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

1. Collaborator

2. CNVs: Variant Details (genomic coordinates and size)

3. CNVs: dynamic percentage filter

*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 on 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 on 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:

1. Curate Variant table is hidden, while Curate Variant page is maximized

2. Curate Variant table is shown, while Curate Variant page is reduced