San Francisco District Attorney Chesa Boudin made the announcement Monday afternoon, saying this is the first prosecution case against a law enforcement officer in the city's history.
A warrant has been issued for former police officer Chris Samayoa's arrest, which Boudin said a judge signed off on Saturday.
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Samayoa has been charged with voluntary manslaughter, involuntary manslaughter assault with a semiautomatic firearm, assault by a police officer and discharge of a firearm with gross negligence.
In December 2017, police said Keita O'Neil carjacked a California State Lottery van and led officers on a pursuit through the Bayview and into a public housing area.
Police said O'Neil then slowed down, jumped out of the van and ran toward the marked police car.
The DA's office said Samayoa shot O'Neil as he ran past the police car.
"As other patrol cars closed in on him and blocked his path, Mr. O'Neil ran past the police car where Officer Samayoa was seated in the passenger seat. Officer Samayoa pointed his gun and shot Mr. O'Neil through the passenger side window of the patrol car, killing Mr. O'Neil," Boudin said in a statement.
Samayoa, the accused officer, had graduated from the police academy just three days before the deadly shooting occurred.
"Body camera footage shows not a single other officer pulled out their service weapon or pointed it at O'Neil," Boudin said.
The officer was fired from the San Francisco Police Department three months following the shooting.
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In a statement released Monday, the district attorney reiterated that police officers are not above the law.
"For too long, we have seen the failures of our legal system to hold police accountable for the violence committed against the members of the public they are entrusted to keep safe," Boudin said
"In SF there has been long history of officer involved shootings leading to no accountability whatsoever, further cementing the idea that police are above the law. That stops today," he went on to say.
O'Neil's relatives were told about the decision to charge Samayoa and O'Neil's aunt, April Green, expressed gratitude, Boudin said in a statement.
"I am happy to hear this news, and hoping it brings some justice to our family," Green said.
Criminal defense attorney John Burris, who represented the O'Neil family, was relieved.
"I was quite pleased to see it," said Burris. "I was a little surprised that it wasn't murder, but I understand the DA thinks manslaughter is a charge that is easier to prove than murder."
ABC7 reached out to Tony Montoya, the president of the San Francisco Police Officer's Association.
"The criminal justice system will allow for the facts surrounding this case to be disclosed. We are committed to ensuring that Christopher and his family are supported during this difficult time and that he is accorded his due process rights and provided with a vigorous defense against these charges," said Montoya in a statement.
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