The collision happened on the AV Line 225 to Lancaster just after 6:30 p.m. in the area of Pine Street and Railroad Avenue.
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Footage from the scene showed the car went through a fence. The driver was transported to a hospital in unknown condition.
There were no immediate reports of injuries among train passengers.
The train was stopped on the tracks and Metrolink service in the area was delayed.
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The circumstances that led to the crash were under investigation.