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Would semi-intelligent, or genetically modifed apes be considered mutants? Or would they be considered abhumans as they are very closely related? My thoughts was hat with the imperium being kinda stupid and all with history, they may not realise the nice little furry monkeys are very closely related to them.

Possibly abhumans...
Though there may be a war before this is realised...
They wouldn't be mutants since they haven't mutated...
Though any ape closely related to humanity would have been on Terra and Terra isn't really an eco-friendly place anymore. It is possible some were taken to other planets during the Diaspora but they seem to have gone extinct as the only reference to them is in comparison to the Jokaero's appearance "Ancient Terran orangutan"
So if there were talking apes they probably wouldn't be all that close to humanity.

If these apes started out as humans and there is no trace of chaos involved, they will be considered abhumans.
If they weren't humans at all, it will depend on their intelligence. If they can still be seen as animals, they will be treated as such. If they show technical skills, they will be considered xenos. Even if they evolved from terran apes, they would be considered an insult to the perfection of the humans and treated like any other xeno race.

As they haven't evolved from humans they are not abhumans and as they have not mutated from humans they are not mutants.

They would however be xenos.