A day after general manager John Lynch said he regretted how he explained his stance on national-anthem protests, the 49ers didn’t have a player kneel or raise a fist during “The Star Spangled Banner” before Saturday’s preseason game against Denver.

As they did in their preseason opener, many of the 49ers stood with the right hand over their chest.

On Friday, Lynch said he’d lost sleep after his comments a day earlier had inspired a mild controversy. Lynch said he thought anthem protests could be “divisive,” but respected players’ right to express themselves.

“If I could take one thing back, I would have changed that word because of the negative connotation,” Lynch said on KNBR. “I was trying to make a point that our game can be a beacon for what should be.”

Lynch said he tried to explain to his 10-year-old daughter last week about the unrest in Charlottesville, Va., which was prompted by a white supremacist rally.

“It’s sad, it’s disgusting, it’s unbelievable that these things still exist,” Lynch said. “… I think I want to go a step further and not only do I respect, but I also understand the motivations of these players that are trying to do something about it. I want to be very clear with that – that’s where my heart is.”

Depth chart: Undrafted rookie safety Lorenzo Jerome and linebacker Eli Harold played with the first-team defense.

Jerome started in place of Jaquiski Tartt, who entered with the second-team defense. After a strong training camp, Jerome had a near-interception and his two tackles includes a strong goal-line stop of running back C.J. Anderson in the open field.

Safety Jimmie Ward (hamstring), who missed training camp, is expected to start alongside Eric Reid when he makes his anticipated return next week.

Harold started in place of Ahmad Brooks, 33, a starter since 2011 who entered with the second-string. Brooks played with the first-team for most of training camp.

Hello, again: There was a common thread among the 49ers’ four game captains: Guard Zane Beadles, running back Kapri Bibbs and linebackers Elvis Dumervil and Dekoda Watson all previously played with the Broncos.

The quartet combined to spend 15 seasons and play 184 games with Denver.

Bowman back: Linebacker NaVorro Bowman played his first game at Levi’s Stadium since sustaining a torn Achilles in a loss to the Cowboys on Oct. 2.

In three series, Bowman had two tackles and broke up a pass to tight end Virgil Green on third-and-6 to end Denver’s second drive.

Sidelined: The 49ers had nine players in street clothes for Saturday’s game: Defensive tackles DeForest Buckner (ankle) and Ronald Blair (groin), wide receiver Aaron Burbridge (hamstring), guard Joshua Garnett (knee), cornerbacks Prince Charles Iworah (unspecified) and Will Redmond (ankle), linebackers Aaron Lynch and Sean Porter (quadricep) and safety Jimmie Ward (hamstring).

Eric Branch is a San Francisco Chronicle staff writer. Email: EBranch@sfchronicle.com Twitter: @Eric_Branch

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