At 9:36 p.m., officials said everyone who was sheltering in place has been escorted out safely and no one was injured in the shooting.
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The incident was first recorded at 5:23 p.m. the Saturday before Christmas and police alerted shoppers and workers to shelter in place.
Sunday morning, Milpitas police said a 22-year-old San Francisco man was injured by a self-inflicted gunshot and was "not the victim of an act of violence."
On Twitter, a shopper posted videos inside the Guess store. Officials asked how many people were inside the store and told them to lock themselves inside.
Another person tweeted video of them running inside a store to take shelter in the back oom.
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Santa Clara Co. Sheriff said crews were on the scene assisting Milpitas police.
Police say there were two unrelated medical emergencies during the evacuations which required medical transportation to a local hospital.
Officials say "there are currently no on-going threats to the community."
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Detectives and field evidence technicians remain on scene and are actively investigating the incident, Milpitas police tweeted.
Those with information on the shooting are asked to contact the Milpitas Police Department.
Stay with ABC7 News for more on this developing story.