William Coffey, 36, was found guilty of rape, sex offenses, sex offenses with a child and indecent liberties with a child.
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He was already on the sex offender registry for molesting another child in 2009.
In court Friday, Coffey's mother said the man is mentally disabled.
In 2015, police said the 6-year-old victim was on her way to the bathroom at the Body of Christ Church on Spring Forest Road in Raleigh when she encountered Coffey in the hallway.
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Coffey allegedly picked her up and carried her into the men's restroom. Court documents said Coffey "covered the mouth of the victim when she attempted to scream." He then raped the girl before letting her leave the bathroom.
At the time, Body of Christ Church said that while it has stringent procedures in place for all personnel working with children, Coffey was not a church member and was visiting a men's Bible study group when the attack happened.
During the sentencing Friday, the judge said: "With respect to rehabilitation, you've had your chance and you've failed."