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EIPR has documented 232 cases between October 2013 and March 2017 where people were arrested for allegedly being gay or transgender, Abd Elhameed said.
Many of these cases went to court where the average sentence was around three years in jail, although in some cases it went up to 12.
At least five such examinations have taken place, Amnesty International says.
Judicial sources do not deny the examinations take place but say they are legally carried out and are not a form of abuse.
A security official would not comment on Hegazy's case but denied that police incite prisoners against each other or otherwise mistreat them.
They incite the other detainees and say 'this girl wants men and women to be gay' so they harass her.
I saw scratches on her shoulder, she looked very disheveled and exhausted.
A 31-year-old gay man recounted how he was tied up and beaten at his Cairo flat last year by two men who threatened to kill him after meeting through the gay dating app Grindr.
They posed as police officers at some point, playing on a common fear for gay Egyptians, before stealing items from his flat.