3. Selecting ACMG CatalogsΒΆ

After the import process the user will be provided with a dialog titled VSClinical ACMG Options, which will be used to define the assessment catalog. The assessment catalog for VSClinical saves finalized ACMG variant classifications and is used as an internal variant database to track variants across projects, including final interpretations and evaluations. If the user already created an assessment catalog for VSClinical, you can choose it from the dropdown, otherwise select Create Catalog.

assessment catalog set up

Figure 3-1: Assessment catalog setup.

For the assessment catalog, the user can define the Database Type. Selecting the different options will provide descriptions into the different types of catalogs. For this tutorial, we will select the SQLite option. Next click Browse and place the folder in a local directory and designate the file name to be ACMG Catalog, click Save. The following dialog should look similar to Figure 3-2. Then click OK. The ACMG Catalog should then be detected in the main interface. Leave all other options as default and select OK.

SQLite

Figure 3-2: Selecting assessment catalog using the SQLite directory.

You will then be prompted with an interface titled Internal Database of Classified ACMG Variants. For this option, open the drop down and select the created ACMG Catalog. This will then finish importing the variants into the project template and load the required annotations in the variant table.

Internal database

Figure 3-3: Internal Database of Classified Germline ACMG Variants.