Recording Interpretation¶
There are a number of features designed to aid in the tracking of the analysis and interpretation of the case and the variants identified. This can be performed on the variant grid and in the interpretation section on the variant details page. These allow for variants to be flagged, commented on, classified and added for export. A history of any comments and classification can be seen in the variants history along with information on who provided the interpretation and when.
Flagging Variants¶
Functionality has been added to allow the ‘flagging’ of variants to highlight variants of interest. Flagging of variants can be done directly from the grid but clicking on the ‘Flag’ icon at the end of the variants row, or in the interpretation section of the variant details page. Filters can be set to show only flagged variants in the variant grid.
Commenting¶
Commenting can be accessed on the variant grid by clicking on the speech bubble at the end of the row. In the variant details page, comments can be added by opening the ‘comments and history’ section in the interpretation section and typing in the text box. Comments will be saved in the variant history along with the person who made the comment and the date and time the comment was made. Comments can only be edited by the person who made the comment and can be done by clicking ‘edit’ alongside the comment made.
Classification¶
A variant classification can be assigned to each variant analysed using the classification column on the variant grid or the interpretation section in the variant details. For somatic small variants the classification system follows the AMP guidelines alongside the biological classification of Benign, Likely Benign, Uncertain Significance, Likely Oncogenic and Oncogenic. For a classification to be saved, both an AMP and biological classification must be selected. For germline variants, the classification is based on the ACMG system and classifies a variant as one of Benign, Likely Benign, Uncertain Significance, Likely Pathogenic and Pathogenic. The classification can be made by selecting the classification from a drop down menu and clicking ‘Classify’ to save. This will also save a record in the variant history with the classification, name of person who classified and time and date. Classifications cannot be edited but new classifications can be made by reselecting from the drop down menu and clicking classify. This will change the overall classification but the prior classification(s) will remain in the variant history.
Add For Export¶
Clicking on the "Add to export" icon on the variant grid or variant details page will add the variant and it's interpretation to the report that can be exported. Refer to Export Preview section for more details.