I've read that in the video game series Overlord, the titular Evil Overlord Player Character was actually born a Chosen One, but the previous Overlord kidnapped him and raised him to become evil. Unlike with Anakin, it was a case of Gone Horribly Right given the Klingon Promotion that followed.
...ahem talk about Conversational Troping
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The Juggernaut is also technically an example, as he is the Chosen One of a god called Cytorrak, who just happens to be an evil god. You can probably find all sorts of examples if you go with that method. It all really depends on who's doing the choosing, y'know?
If you're only interested in Chosen Ones explicitly chosen by forces of good and nonetheless turn "evil," that's harder to find. Even Anakin might not count as an example given that the Force explicitly has a dark side. Ardyn Izunia of Final Fantasy XV might count, but it's still unclear whether he was actually chosen as opposed to "choosing" himself. Apparently, there's a good chance that'll be cleared up by year's end.