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

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

• Otherwise, you will see an Export to Curate button instead.

Where can I find Curate annotations?

1. Variant table > Known Variants column > 👁️ Curate Pathogenicity** badge**

1. Variant page > Summary section > Clinical Significance card > 👁️ Curate Pathogenicity** badge**

1. Variant page > Clinical Significance section > Clinical Significance card > 👁️ Curate Pathogenicity** badge** and a link to the Curate Variant page

1. Variant page > Clinical Significance section > Variant info card > Transcript > 👁️ The Curate** transcript** is marked with a Curate logo

1. Variant page > Evidence section > Pathogenicity box > 👁️ The Curate Pathogenicity stored in Curate is marked with a Curate logo

1. (34.0+) Variant page > Visualization section > 👁️ Curate and CurateSV Curated data tracks (make sure to enable tracks of interest)

1. Manually add a new variant in Curate

2. Export from the Variant page

Manually add a new variant in Curate

To manually add a new variant:

1. Click on the *Add new variant/gene button,

2. Select a desired human genome assembly,

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

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

Export from the Variant page

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

1. Tag the variant,

2. Set a Pathogenicity,

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

Note: Only users with a specific role have permission to export variants to Curate.

The Curate Variant table lists the variants stored in your database.

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.

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

The Curate Variant page presents the most clinically relevant variantinformation.

The Curate Variant page is comprised of:

Top bar

that lists:

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

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

3. Variant effect,

4. Pathogenicity. Note: you can change Pathogenicity by selecting a different option from the dropdown menu.

Interpretation section

that features:

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

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

Note: to edit your notes, select thetab (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 section

that includes:

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

2. The currently selected condition,

3. Links to data sources,

4. Inheritance mode icons where available,

5. A Change button that opens the disease selection menu.

Variant information section

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.

Related Cases section

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 annotation overlap percentage filter,

4. CNVs: Annotation Overlap;

5. Previously assigned Pathogenicity,

6. Case creation Date,

7. Previously assigned variant Tag,

8. Variant Inheritance,

9. 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 section

that shows, for each occurrence of the variant in each Curate database maintained by collaboratorswithin your Network:

1. Collaborator,

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

3. CNVs: dynamic annotation overlap percentage filter,

4. CNVs: Annotation Overlap;

5. Pathogenicity,

6. Case creation Date,

7. SNVs: Transcript,

8. Gene Related Disease,

9. 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 section 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 iconon 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.

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 variantinformation (right).