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  • San Francisco 49ers linebacker Reuben Foster appears for his arraignment...

    San Francisco 49ers linebacker Reuben Foster appears for his arraignment at the Santa Clara County Hall of Justice in San Jose, Calif. on April 12, 2018, where he answered to felony domestic violence and weapon charges. (Dai Sugano/Bay Area News Group)

  • San Francisco 49ers linebacker Reuben Foster, center, heads into the...

    San Francisco 49ers linebacker Reuben Foster, center, heads into the courtroom for his arraignment at the Santa Clara County Hall of Justice in San Jose, Calif. on April 12, 2018, where he answered to felony domestic violence and weapon charges. At right is Foster's attorney, Joshua Bentley. (Dai Sugano/Bay Area News Group)

  • San Francisco 49ers linebacker Reuben Foster, center, heads into the...

    San Francisco 49ers linebacker Reuben Foster, center, heads into the courtroom for his arraignment at the Santa Clara County Hall of Justice in San Jose, Calif. on April 12, 2018, where he answered to felony domestic violence and weapon charges. In the background is Foster's new teammate, Richard Sherman, one of two 49ers' teammates who attended the arraignment. (Dai Sugano/Bay Area News Group)

  • San Francisco 49ers linebacker Reuben Foster, center, stands next to...

    San Francisco 49ers linebacker Reuben Foster, center, stands next to his attorney, Joshua Bentley, during his arraignment at the Santa Clara County Hall of Justice in San Jose, Calif. on April 12, 2018, where he answered to felony domestic violence and weapon charges. (Dai Sugano/Bay Area News Group)

  • San Francisco 49ers linebacker Reuben Foster, center, leaves from the...

    San Francisco 49ers linebacker Reuben Foster, center, leaves from the Santa Clara County Hall of Justice after his arraignment in San Jose, Calif. on April 12, 2018, where he answered to felony domestic violence and weapon charges. (Dai Sugano/Bay Area News Group)

  • Reuben Foster, San Francisco 49er linebacker, leaves Santa Clara County...

    Reuben Foster, San Francisco 49er linebacker, leaves Santa Clara County Jail, Sunday evening, Feb. 11, 2018, after being arrested on suspicion of domestic violence and possession of an assault rifle in Los Gatos. (Karl Mondon/Bay Area News Group)

  • In this Oct. 22, 2017 file photo, San Francisco 49ers...

    In this Oct. 22, 2017 file photo, San Francisco 49ers linebacker Reuben Foster (56) stands on the sideline during the second half of an NFL football game against the Dallas Cowboys in Santa Clara, Calif. (AP Photo/Marcio Jose Sanchez, File)

  • LINEBACKER: Shane Vereen #34 of the New York Giants is...

    LINEBACKER: Shane Vereen #34 of the New York Giants is tackled by Reuben Foster #56 of the San Francisco 49ers during their NFL game at Levi’s Stadium on November 12, 2017 in Santa Clara, California. (Ezra Shaw/Getty Images)

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Cam Inman, 49ers beat and NFL reporter, San Jose Mercury News, for his Wordpress profile. (Michael Malone/Bay Area News Group)
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SANTA CLARA — Reuben Foster’s status with the 49ers remains in jeopardy, and general manager John Lynch finally outlined why he’s still around despite three felony charges including a domestic-violence allegation.

“I do want to be very clear, abundantly clear, if these charges are proven true, if Reuben did indeed hit this young lady, he won’t be a part of our organization going forward,” Lynch said Monday in his first remarks since Foster was arraigned April 12 in Santa Clara County Superior Court.

“The gravity of these charges has not been lost on us. We take it extremely seriously. We do feel like patience is the right approach right now,” Lynch said. “We’re going to learn things through this legal process.”

San Francisco 49ers linebacker Reuben Foster appears for his arraignment at the Santa Clara County Hall of Justice in San Jose, Calif. on April 12, 2018, where he answered to felony domestic violence and weapon charges. (Dai Sugano/Bay Area News Group)
San Francisco 49ers linebacker Reuben Foster appears for his arraignment at the Santa Clara County Hall of Justice in San Jose, Calif. on April 12, 2018, where he answered to felony domestic violence and weapon charges. (Dai Sugano/Bay Area News Group) 

Foster has an April 30 court date to either make a plea or, more likely, seek to push that to a later date. He is charged with domestic violence with an allegation that he inflicted great bodily injury against his live-in girlfriend, forcefully attempting to prevent a victim from reporting a crime, and possession of an assault weapon.

Lynch acknowledged he and team officials were surprised at prosecutors’ accounts of the Feb. 11 incident that led to Foster’s arrest.

“Yeah, that could be said for all of us,” Lynch said. “But again we felt after we sat back after that and took account of what happened, we felt there’s still reason to wait, and that’s what we’re doing.

“We abhor domestic violence. I don’t think anyone likes it. … We have a team policy. The team policy is to look at everyone’s situation as unique.”

In this Oct. 22, 2017 file photo, San Francisco 49ers linebacker Reuben Foster (56) stands on the sideline during the second half of an NFL football game against the Dallas Cowboys in Santa Clara, Calif. (AP Photo/Marcio Jose Sanchez, File)
In this Oct. 22, 2017 file photo, San Francisco 49ers linebacker Reuben Foster (56) stands on the sideline during the second half of an NFL football game against the Dallas Cowboys in Santa Clara, Calif. (AP Photo/Marcio Jose Sanchez, File) 

Foster is not participating in the 49ers voluntary offseason program that began a week ago, and he won’t be welcome at the team facility through the June minicamps, Lynch said. Foster faces at least a six-game suspension under the league’s personal-conduct policy regarding domestic violence cases.

Fellow linebacker Malcolm Smith said of Foster’s absence: “Obviously he’s going through some issues and legal stuff but we definitely miss his spirit in our group.”

Left tackle Joe Staley, the 49ers’ longest-tenured player as a 12th-year veteran, praised the 49ers front office for communicating with the team how they’re handling Foster’s predicament and it’s implications.

Said Staley: “They made it very clear: if he did what’s he’s being accused of, he’s not going to be here. So that’s a message to anybody: keep yourself out of trouble in the offseason, do right by those around you.”

Added Lynch: “It’s one player. One of the great lessons I’ve learned in this league is nobody is bigger than the team. If we learn that the charges that have been levied against them, if we learn them to be true, he’s not going to be here, and I think that speaks volumes.”

Selected 31st in last year’s draft, Foster was the 49ers second-leading tackler despite missing 7 of 16 games to injury.

The NFL, rather than the 49ers, has been in charge of investigating Foster’s case, per the league’s 2016 amendment to its personal-conduct policy regarding domestic violence accusations. Foster, now that he’s been formally charged, could be placed on the Commissioner Exempt List, but only at the appointment of NFL commissioner Roger Goodell. Lynch said the 49ers remain in contact with the league regarding that potential.

— Quarterback Jimmy Garoppolo is conducting extra throwing sessions with his receivers on the weekend, away from the team facility and without coaches’ supervision. Their first such session was last Saturday, and Garoppolo declined to reveal where. He noted he’s been doing such side work since high school.

“It’s just something I like to do,” Garoppolo said. “It gets us away from the coaches and allows me to talk to receivers about specific things, and tight ends and running backs. We had a great showing this Saturday. … Talking through route concepts, how they see it, how I see it, it gets us on the same page.”

— Safety Eric Reid’s tepid reception in free agency means he still could re-sign with the 49ers. Lynch said they’ve been in communication with Reid, addding: “It’s just the safety market has been incredibly slow and Eric’s been a victim of that. … Some of that is Eric’s discretion of where he wants to be. We won’t close the door on that.”

— Jimmie Ward is embracing his return from safety to outside cornerback, where he last played full-time in 2016 in what he describes as a vastly different scheme. Ward believes his ultimate position will be determined by who the 49ers draft this week, but he likes his versatility and has a personal goal of recording an interception at cornerback, nickel back and safety.

— Lynch remained non-committal on whether the 49ers will exercise the 2019 options for defensive lineman Arik Armstead and left guard Laken Tomlinson, a pair of 2015 first-round draft picks. Armstead, Lynch said, will likely line up at “big end” on base downs and move inside rather then replicate his 2017 role as a “Leo” pass rusher. Solomon Thomas, last year’s top draft pick, could play the “Leo” role on first down before also shifting inside, Lynch said.

— Lynch said 12 draft prospects have Pro Bowl potential and the 49ers have first-round grades on 30 players, including quarterbacks, although they don’t need one thanks to Garoppolo.