Yesterday, I said I couldn’t think of a good example of a definitively genderless human character in anime. But I can easily name one from an anime-style video game: Subaru Kujou from Sakura Taisen V, also known as Sakura Wars: So Long My Love.
Subaru actually outright says that gender isn’t important and certainly seems to be portrayed as not wanting to identify as either male or female.
Subaru’s physical sex is never really made clear, but it’s implied to be something other than ‘typical’ female a few times. Subaru alludes to having a reason beyond shyness for not joining the others (women) in the bath, won’t change clothes in front of anyone, and even seems to be immune to one villain’s power that only works on women.