There is a lot of confusion about the meaning of the term gender. In academia (and LGBT vernacular) gender is something different than sex.
When a trans person shares their gender with you, this does not mean they are unaware of their birth (or current) sex. However, they prefer to be treated the same way you’d treat a cis person of that gender.
What this means depends on the individual, but you can start by respecting their pronouns, now that you know what they mean when they use them. I hope this clears things up a little bit.