This character suffers from Gender Dysphoria.

Gender dysphoria is a term that describes a sense of unease that a person may have because of a mismatch between their biological sex and their gender identity. This sense of unease or dissatisfaction may be so intense it can lead to depression and anxiety and have a harmful impact on daily life.

Only apply the trait if the character is explicitly mentioned to have gender dysphoria in the visual novel. So, a transgender person who never mentions this shouldn't have the trait applied.