The agency’s fee is applied to the rewards that your delegation yields.

APR (Annual Percentage Rate) represents how much you will earn from that investment in one year. For example, if a validator currently receives a 12% APR and charges a 10% fee, his delegators will receive a 10.8% APR.

Basically, for every 100 EGLD that you stake, you will be rewarded with another 10.8 EGLD yearly.

This is without taking into account reward compounding opportunities. If the rewards are compounded, the rewards can grow higher.