When you want to delete a Subordynary/Parent linked Template, you will need to go through the following 4 steps.
You want to delete the Item Varient Template
1. Go to the Data Templates list, and select the parent linked Template
2. Set template status to "Under Development" and go to "Subordinary Data Template"
3. Delete "Item Variant"
4. Go to the Data Templates list, and delete "Item Variant"