By News Director Jared Atha A Clinton man has been charged with first degree rape after allegedly having sexual intercourse with a 13-year-old girl. According to the probable cause affidavit, 21-year-old Brandon Lee Thomas was arrested and charged in Custer County with the crime after police were made aware of the inappropriate relationship by the victim’s father. The court document stated that the father first became aware of the relationship after the school had contacted his wife about it. The father would search the child’s phone and found inappropriate messages from Thomas to the youth. The father says that when he approached the girl about the messages and the relationship with Thomas, she told him that on February 1, Thomas had come to their home and had allegedly raped her.