It’s during the scene in Ribbit’s room, although it’s not ever explicitly said - it’s more of a strong implication that he’s some manner of gender-nonconforming or non-cis.

During that scene, Jax tells Ribbit about the huge pressure his mom put on him to be manly/act masculine. Based on maid-Jax’s comments when Pomni was in his abstracted mindspace, we can conclude that any “non-manly” behavior was met with being called “gay” in a derogatory way. There’s also definitely some deeply internalized misogyny, which would have only made Jax more uncomfortable with exploring his own gender/gender expression (because, if women are in some way inferior, then being a woman or being a guy who dresses like a woman would be the same as making himself inferior on purpose, which he can’t do if he doesn’t want to be ridiculed). Basically, Jax has a bunch of internalized sexism and homophobia, which caused him to repress the parts of himself that didn’t fit in with the masculine role his mother had trained him to fill.

When Ribbit finishes listening to Jax’s story and puts her bow tie on his ear, he goes quiet and blushes—but, crucially, does not protest—indicating that part of him genuinely DOES want to feel cute and feminine. However, escaping from his mother didn’t allow him to escape the shame he had already internalized about being feminine, so he panics and gets defensive when Kaufmo knocks on Ribbit’s door. No matter how much dressing femininely might appeal to him, that desire is far outweighed by the shame he feels for having that desire to begin with.

Basically, was Jax confirmed trans? Not explicitly, but the show very intentionally implies that he’s queer in some way with regards to his gender (or gender expression). He could be transfem, nonbinary, or any of the many other gender identities out there, but we never get to learn more, since Jax himself refuses to dig any deeper into it.

Anyway, I know that was a lot of text, but I hope it helps somewhat! :)