Police say the driver, identified as 28-year-old Jamar Henry, picked up the 7-year-old boy from Cornerstone Christian Academy at 58th and Chester streets Monday afternoon.
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Henry then stopped at the Shop Rite supermarket at 67th Street and Haverford Avenue, police say, where he allegedly told the child to stay on the bus while he went inside the store.
A passerby noticed the child alone on the bus and called police.
Investigators say that while officers were talking to the child, Henry came running out of the store, telling officers he had a bathroom emergency and needed to stop.
However, police say, surveillance video from the store did not back up Henry's claim.
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Henry was taken into custody and charged with endangering the welfare of a child. He was also charged for possession of marijuana.
The boy was not hurt in any way and has been returned to his parents.