Can I have protective variants and risk variants at the same time? How can this be interpreted?

Yes. The estimation of genetic risk involves considering all the variants related to the condition that an individual possesses. Each described variant related to a trait or complex condition has a “weight” on it. Therefore, the genetic risk will ultimately depend on the type of variants and which weight predominates in their results.

If you have few risk variants, but these have a very significant weight in the development of the condition, despite having many protective variants, it is highly likely that an individual will have a high genetic risk of developing the condition.