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Linebacker Fred Warner has been 49ers’ biggest surprise

Fred Warner played with an aching back and throbbing wrist for most of his freshman season at BYU.

As it turns out, it was more than a bump and a bruise: Warner was tackling running backs with a stress reaction in his lower back that became a full-blown fracture, and fending off blockers with a broken wrist.

How did he do that? The 49ers’ rookie inside linebacker smiled and shook his head after matter of factly detailing his painful season.

“Yeah, looking back, it was pretty crazy,” Warner said. “I don’t even think about it that much anymore — but just talking about it is pretty wild.”

Warner’s freshman year spoke to his grit, but it didn’t prevent pre-draft questions about his ability to handle the rigors of playing inside linebacker in the NFL.

Months later, however, his first nine games have done the trick.

Warner, 21, spent much of his time in coverage in college, which prompted doubts about his physicality and durability. Nevertheless, he has held up well as a traditional linebacker: The third-round pick ranks fifth in the NFL in tackles (73). He’s on pace for 130, which would be the most by a 49ers player since NaVorro Bowman’s 154 in 2015.

In addition, Warner (6-foot-3, 226 pounds), has been the definition of durability, despite being light for his position.

He leads the 49ers in defensive snaps (591 of a possible 597), having played 118 more than tackle DeForest Buckner, who ranks second. Warner is also one of eight NFL linebackers — and 32 defensive players — to be on the field for at least 99 percent of his team’s plays this season.

Warner played the 49ers’ first 591 snaps before his streak was snapped when he was replaced late in a 34-3 win over the Raiders on Nov. 1.

He has yet to appear on the injury report this season, but he indirectly acknowledged playing his position has exacted a physical toll. Unlike his first season in college, though, Warner presumably isn’t playing with any broken bones.

“Shoot, the NFL has a 100 percent injury rate, so at some point, you’re going to get hurt,” Warner said. “But it’s about playing through soreness and the bruises and nicks you get.”

Warner is proud of his durability. And he’s shocked he has had a chance to display it so quickly in his career.

During Warner’s pre-draft visit, special-teams coach Richard Hightower showed him the team’s inside-linebacker depth chart, headlined by Reuben Foster and Malcolm Smith, and told him he’d be playing plenty of special teams if the 49ers drafted him. Early in the offseason, cornerback Richard Sherman told him to stay patient and prove himself on special teams.

Iron Men

Fred Warner is one of eight linebackers who has played at least 99 percent of his team’s defensive snaps this season:

Kiko Alonso, Dolphins: 100 percent

Jordan Hicks, Eagles: 100

Myles Jack, Jaguars: 100

Lavonte David, Buccaneers: 99.6

Tahir Whitehead, Raiders: 99.4

Telvin Smith, Jaguars, 99.2

Avery Williamson, Jets: 99

Fred Warner, 49ers: 99.0

Source: ProFootballReference.com

“If you told me before the season that I was going to be playing every single snap, I would you have thought no way,” Warner said. “But this has been a great learning experience.”

Warner quickly made it clear he wasn’t soft. And that extended to his voice.

In the spring, head coach Kyle Shanahan joked that Warner was relaying the defensive signals at such a high decibel that he could be heard in the offensive huddle. In training camp, during one of the first padded practices, Warner leveled fullback Kyle Juszczyk, prompting tight end Garrett Celek to note: “That guy knows how to hit.”

At BYU, Warner played a hybrid position that included elements of linebacker, safety and nickel cornerback. It showcased his overall abiltiy, but not an ability to consistently make tackles near the trenches.

His younger brother, Troy, a junior defensive back at BYU, was Fred’s teammate in college and at Mission Hills High-San Marcos (San Diego County). And he also tussled with his brother and best friend growing up.

“Fred being tough and playing hurt — that’s never been an issue,” Troy said. “That’s something he’s shown throughout his football career.”

The best example came during his first season at BYU.

Warner played five games with severe discomfort in his lower back. The pain gradually increased until it became unbearable: A UNLV offensive lineman ended his season by drilling him when Warner was lying face-down in a late-season game. Warner spent more than three months in a carbon-fiber brace that extended from his chest to his waistline.

During his treatment for his back, Warner mentioned his wrist had been bothering him since he tweaked it in a preseason practice. The result: surgery to repair the previously unknown break.

“It wasn’t fun at all playing with it,” Warner said of his wrist. “I would tape it up so tight because I didn’t know any better. I would tell the trainers: ‘Yeah, tape this one up really tight.’ Shoot, I would be hitting people and I could feel stuff shifting in there. I would shake it off and keep going.”

Warner, who wasn’t a full-time starter at Mission Hills until his senior year, learned about perseverance from his mom, Laura.

She and her husband, Fred Sr., divorced when Fred was a toddler and she raised Fred, Troy, and their sister, Maya, 16, while working as a secretary at a law firm. Warner said the family received assistance from churches and extended family, such as uncles who purchased cleats and gloves.

“We had a lot of people who were willing to help us along the way growing up,” Warner said. “There were some times it was pretty rough. My mom made sure we were always provided for. Looking back, I know my mom sacrificed a lot for us.”

Those sacrifices helped Warner reach the NFL, in which he has assumed responsibilities that belie he’s the 49ers’ youngest player.

Warner reportedly had the highest score (32) among linebackers at the combine on the Wonderlic intelligence test. His smarts are a reason he has relayed the defensive play calls to his teammates as a rookie.

Warner has the “green dot” on his helmet, which means he wears the radio headset through which defensive coordinator Robert Saleh relays plays.

“There’s a lot that goes into wearing a green sticker and calling plays,” Sherman said. “Sometimes the mike gets cut off in the middle of a play call and he has to improvise. Sometimes the offense hurries to the line and he has to call a play. All 10 guys are looking at him. He’s done a phenomenal job, though. He’s stayed locked in. He’s stayed poised. He knows situations, and you’ve got to tip your cap to him.”

Warner is a reason the 49ers have had a respectable run defense in a 2-7 season. They rank eighth in yards allowed per carry (4.0) and 12th in rushing yards allowed per game (102.8).

Still, there remains room for improvement. Most notably, both Saleh and Warner acknowledge he too often has been engulfed by offensive linemen on run plays.

“Sometimes I get down on myself on little things I mess up on,” Warner said. “I’m hard on myself. And I know coaches are going to be just as hard on me.”

After nine games, though, Warner has proven this: He’s tough enough to take it.

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



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