It varies from person to person. Sometimes it’s stuff like body dysphoria (MRI’s show that trans peoples biological sex don’t match the sex of the brain, likely the brains mapping of the body is therefore often somewhat incorrect), sometimes there is just a feeling, sometimes there is a noticeable comfort or discomfort with presenting this or that way, sometimes there are thoughts and dreams, sometimes there are behavioral or mental effects.

How people react to going through puberty can be telling as well, as it seems the brain is kinda programmed to want a certain mix of hormones. Some trans people report a variety of shitty mental symptoms going away when receiving hrt, and coming back when stopping. Some react very negatively to the physical changes brought on by puberty.

I remember day dreaming about finding out that I’m intersex (I didn’t know the term, I had just heard about something similar happening somewhere) and a doctor telling me I could choose to be a girl when I was a kid. I would always pick female characters in video games, it was always just harder to be invested in male characters even if they were never visible. I would always make them look like what I imagined I would look like as a girl/woman.

I had my mom dress me up as a girl for halloween once and have had a number of cross dressing occasions throughout my childhood.

I never liked having short hair and frequently let it grow out. I was always jealous of the clothes girls got to wear.

I never really clicked with guy stuff, though I didn’t have very feminine hobbies or interests either. Stuff that was male-coded was however extra unappealing to me just because it was male-coded.

The idea of being very masculine was extremely unappealing, and I was secretly very proud and happy of every comment and compliment I received about behaving feminine or being non-masculine.

I was casually a woman in 50% of my daydreams and was always fascinated by fiction involving swapping genders and being accepted for who you were etc.

I don’t like my face or my beard all that much despite looking perfectly alright, and I really disliked having any body fat at all (I don’t mind a healthy bit of body fat nearly as much now that my hormones tell my body to store it in feminine places).

Anyways, I never really suspected I was trans until like a year ago despite feeling kinda text book in hindsight.

EDIT: Hope the wall of text isn’t overwhelming. The TLDR is it’s complicated, and the only way to know is to just know or try stuff out until you feel comfortable :)

EDIT 2: I figured out I was trans by reading the definition and symptoms, thinking about it for a couple of months, and then trying some stuff out.