Variant Filters

The Variant Filters section describes how to add, configure, duplicate, or archive variant filters.

Add and Configure a Variant Filter

1. On the top toolbar, select Configuration.

2. Select the Test Components tab.

3. Navigate to Variant Filters and select New.

4. Navigate to the Condition Group section and enter the applicable genes in the Genes field.

5. [Optional] Select the Include genes from diseases check box.

6. Select Apply.

7. Select Include or Exclude from the drop-down list for each gene.

8. For Variant Category, select the field to open up a drop-down list of variants that can be included or excluded.

9. Select the check boxes next to the applicable variant types.

10. Select Add Criteria and select the applicable criteria from the drop-down list (for example, Cancer Hotspot Samples).

11. Select Include or Exclude from the drop-down list for the criteria.

12. To include or exclude additional criteria, repeat steps 10 and 11.

13. For AND or OR, select Add Condition Group to add any other applicable condition groups.

14. [Optional] Select Reset to undo the changes to the condition groups.

15. Select Save.

The Genomic Region criteria is not available when creating a filter from configuration but can be included when adding/editing filters in Variant grid . For more information, refer to Add and Configure a Variant Filter.

Edit a Variant Filter

1. On the top toolbar, select Configuration.

2. Select the Test Components tab.

3. For Variant Filters, select a filter.

4. Select Edit.

5. Update the applicable settings. For more information, refer to Add and Configure a Variant Filter.

6. Select Save.

Duplicate a Variant Filter

1. On the top toolbar, select Configuration.

2. Select the Test Components tab.

3. For Variant Filters, select the applicable filter.

4. In the right-hand pane, select Duplicate.

5. [Optional] Adjust the condition group settings. For more information, refer to Add and Configure a Variant Filter.

6. Select Save.

Archive a Variant Filter

1. On the top toolbar, select Configuration.

2. Select the Test Components tab.

3. For Variant Filters, select the applicable filter.

4. In the right-hand pane, select Archive.

5. To confirm, select Yes, change.

Default Filters

Connected Insights provides the following default filters to assist in preliminary test implementation:

All Demo	Filters for oncogenic, likely oncogenic, 1A, 1B, and 2C small variants, copy number variants, unidirectional gene fusions, and RNA splice variants.
SNV Demo	Filters for oncogenic, likely oncogenic, 1A, 1B, and 2C small variants.
CNV Demo	Filters for oncogenic, likely oncogenic, 1A, 1B, and 2C copy number variants.
SV Demo	Filters for oncogenic, likely oncogenic, 1A, 1B, and 2C unidirectional gene fusions.
RNA Splice Demo	Filters for oncogenic, likely oncogenic, 1A, 1B, and 2C RNA splice variants.
AML Demo	Filters for AML-related variants based on WHO 2022 and ELN 2022 guidelines.