The incident happened around 1:30 a.m. Sunday morning on Bayshore Boulevard and Sunnydale Avenue and a man was pronounced dead at the scene.
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Officials say while the train was stopped and waiting for the light at the last stop, a man on the platform approached the train and tried to open the doors.
"Preliminary information indicates that the deceased sat on the couplers between two LRV cars while the train was stopped," police said in a news release. "He fell underneath the second car of the train once it started moving again."
When the operator started to turn the train around, the man fell off the platform and the second car of the train hit him.
The SFMTA says the operator did not know of the collision. Another operator reported the body on the tracks.
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The Municipal Transportation Agency says "this is the first incident for us of this nature in approximately two years.
The scene was cleared around 7 a.m. and SFPD and Muni Systems Safety continue to investigate the incident.
In a statement, SFMTA sends their "deepest condolences to the family and friends of the man struck this morning."
The coroner's office will make the official determination of the cause of death.
Police said the investigation is ongoing and ask anyone with information to call the tip line at (415) 575-4444.