12. VSClinicalΒΆ

The ACMG Guidelines tab will open the main Classifications page in the center and the variant information in the sidebar.

The ACMG Guidelines evaluation screen

Figure 12-1: The ACMG Guidelines evaluation screen.

The collapsible right sidebar can be used to switch the evaluation to other variants as well as see summary information about the current variant. Although only one variant was pulled into this evaluation, each variant is represented with a box with the variant names available on hover. The boxes are filled in when the variant is evaluated and saved. The color scheme is as follows.

ACMG Guidelines pathogenicity color scheme

Figure 12-2: ACMG Guidelines pathogenicity color scheme .

Each variant is automatically evaluated by the ACMG recommendation engine, with many of the individual criteria receiving recommendations on whether it should be answered Yes or No as well as detailed reasons for these recommendations.

In the Evidence Summary section, criteria that are recommended will be listed under Recommended to Score Pathogenic and Recommended to Score Benign. The name of the recommended criteria are in colored bubbles with arrow links to navigate to the tab and section containing the criteria question and supporting evidence.

Criteria questions are organized in the following tabs located at the top of the interface: Population, Gene Impact, Studies, and Clinical. In the following pages of this tutorial, we will go through the tabs to evaluate the SMAD4 variant that will take us through these tabs. As we answer criteria questions, note how the right bar ACMG Scoring section will update with the currently scored criteria and the resulting ACMG Classification.

ACMG Classification

Figure 12-3: ACMG Classification side bar.