The Pennsylvania Office of Attorney General filed the charges against 37-year-old Kendall Stephens.
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Sources tell WPVI Stephens raped two boys under the age of 13. Further details on the investigation have not been released.
Some of the charges include indecent assault against a person less than 13 years old, rape, unlawful contact with minor sexual offenses, and endangering the welfare of children - parent or guardian.
A judge set her bail at $250,000 and her next court appearance is scheduled for December 29.
The AG's office often takes on cases from local district attorneys if they have a conflict in the case.
In a statement to WPVI, a spokesperson for the Philadelphia District Attorney's Office says, "The investigation of allegations against her is being led by another agency, and as such we have no comment."
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The prominent LGBTQ+ activist came to Action News in August of 2020 after she was attacked in her Point Breeze neighborhood. She says she was targeted by a violent group for being a trans woman.
Stephens then became a prominent activist for the LGBTQ+ community and she urged lawmakers to change Pennsylvania's hate crimes statute to include protections for LGBTQ+ people.
WPVI was there for a 2021 press conference where Stephens, along with several other activists, stood by District Attorney Larry Krasner to help launch the LGBTQ+ Advisory Board.
The board was created in part to be a source of information and resources for victims and survivors of crime, within the community.