Yes. The genetic risk estimation consists of taking into account all the variants related to the condition that an individual possesses. Each described variant related to a complex trait or condition has a "weight" on it. Therefore, ultimately, the genetic risk will depend on the type of variants and which weight predominates in your results.
If you have few risk variants, but these have a very important weight in the development of the condition, despite possessing many protective variants, it is highly likely that an individual will have an elevated genetic risk of developing the condition.