SANTA CLARA, Calif. -- With the offseason issues surrounding San Francisco 49ers linebacker Reuben Foster, it was all but certain the team would spend one of its nine selections in the draft on a linebacker.

The question wasn't whether the Niners would take a linebacker, but how early. Throughout the pre-draft process, the Niners were consistently connected to Georgia's Roquan Smith and Virginia Tech's Tremaine Edmunds.

But there was another linebacker with whom the 49ers never hid their interest throughout the run up to the draft and who became the first of their two third-round picks: BYU's Fred Warner.

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Warner wasn't the draft's top-ranked linebacker, but he might have been the best fit for the 49ers. This is why general manager John Lynch said Warner would have been a priority regardless of Foster's legal issues.

"Fred Warner probably would have been drafted by us had Reuben not had any situation at all," Lynch told 95.7 The Game radio in San Francisco. "We wanted to continue to improve at that position, but I think Reuben’s situation probably put even a little more emphasis on, 'We need to find someone there.'"

The 49ers believe they've found is a player with the athleticism and intelligence who's an ideal fit for one of their two inside linebacker positions. In San Francisco's scheme, the WIL and MIKE linebacker spots are both considered "inside" and interchangeable. In fact, coach Kyle Shanahan said the primary difference between the two spots is the MIKE has more to do in terms of communication.

At the team's rookie minicamp last weekend, Warner got his first action as the middle linebacker, hardly a surprise given the Niners' affinity for his football IQ. Warner scored a 32 on the Wonderlic and impressed Lynch with his intellect so much that Lynch joked Warner could "moonlight at Google" when he's not playing football.

"One thing he does, we play a lot of zone defense, you have to read the quarterback," Lynch said. "You have to see the quarterback, and when that hand comes off, you break. There's just numerous clips that kind of fit what we do, and he's a guy we just all really appreciated the more and more we watched. Then he's just kind of got that same makeup."

Warner added to that by running a 4.64 40-yard dash and leaping 38.5 inches in the vertical jump at the NFL combine.

“We want linebackers who can run," Shanahan said. "We put them in some tough spots. They have to cover a lot of ground in what we call the hook area; it's from hash to hash and almost to the inside edge of the number. So that's a lot of space that you have to key the quarterback and to get under things, so the quarterback has to check it down over the ball, and then you need the quickness and the tackling ability to close.”

Those types of linebackers are also becoming more en vogue in today's NFL. While Warner acknowledged his familiarity with a 49ers' linebacker lineage that includes the likes of Patrick Willis and NaVorro Bowman, he's cut from a cloth similar to a new breed of linebackers around the league who don't weigh much -- Warner was 236 pounds at the combine -- but can run, cover and hit like safeties.

Warner never played safety at BYU, but he did play a sort of hybrid position that had him lining up in the slot the majority of the time. Technically, the position was the SAM linebacker, but Warner said the Cougars called it the "Flash." Against teams that used multiple-tight end packages, Warner played a more traditional linebacker role. But against teams that liked to spread things out, he was effectively playing the nickel position.

"It’s something that just kind of came natural to me, and my coaches had a lot of trust in me to be out there in space to cover guys, cover slot receivers, cover tight ends, and it’s only added to my game," Warner said. "I feel like that’s one of the hardest things you can ask a linebacker to do, so I’m happy to have that."

In certain scenarios as the "Flash" linebacker during his time at BYU, Warner was essentially operating as a nickel cornerback in pass coverage. Greg Thompson/Icon Sportswire

Among the questions surrounding Warner that allowed him to fall to the third round was where, exactly, he fits in the NFL. The Niners had no such concerns after observing how some players with similar skill sets have fared in defensive schemes like their own. Warner has drawn comparisons to Jacksonville's Telvin Smith, Atlanta's Deion Jones and Seattle's Bobby Wagner.

From that group, Warner is closest in size to Wagner, who weighs 245 pounds. It's a comparison Niners defensive coordinator Robert Saleh mentioned to Shanahan in pre-draft tape study. Saleh would know, for he worked with Wagner in Seattle.

"This is a passing league now, and teams are passing the ball about 65 percent of the game, and you have got to have linebackers who can move and cover right now. That’s kind of why I feel like I fit perfect in what we’re doing," Warner said.

For now, Warner is working in the middle, but he figures to get snaps at both inside linebacker spots. Warner has also made it a point to study players such as Jones and Smith, recognizing that he will be asked to do many of the same things in the NFL.

"Those are kind of like the new-age linebacker," Warner said. "They’re not the big bruisers. They’re kind of the smaller guys who can run and cover, and they’re physical dudes, too."

Of course, Warner has a long way to go to prove he can be as productive as the players to whom he has been compared. But he might have one advantage over all of them in that pursuit: While he is similar in weight, he's also 6-foot-3 with 32-inch arms that allow him to be even more of a nuisance in passing lanes.

"Maybe it’s just the next step, I don’t know," Warner said.