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SANTA CLARA – Maybe it was obvious the whole time that the 49ers would take three quarterbacks. Kyle Shanahan had made it clear that he’s satisfied with either one of Nick Mullens and C.J. Beathard as the team’s backup and there is a genuine value in having a capable backup quarterback.

But the upside of the extra roster spot created by taking two quarterbacks – the team’s preference and precedent set in each of the last two seasons – probably distracted from Beathard’s internal value to the team.

For as underwhelming as Beathard often is (1-9 with 12 TD, 13 INT in career), he is far from incapable, and does, as Shanahan has said, possess a consistent deep threat. He demonstrated that against the Denver Broncos and was robbed of a massive play by a drop from Kendrick Bourne on a perfectly placed pass.

The idea of cutting Beathard was probably never in play for the 49ers (especially considering the team’s unwillingness to part with recent draft picks – although Joshua Garnett may soon prove to be an exception to that standard), and when things like Andrew Luck’s shock retirement happen, it makes that approach look shrewd. But there is a problem with keeping three quarterbacks on the roster, especially for a team as injury-prone as the 49ers.

A trade is in the card for Beathard, but if it’s not genuine value (like a capable offensive lineman and/or draft picks), Beathard’s going to stay put as the number three. And even if a trade does come, it may well be after cut down day, leaving the 49ers needing to get creative with a few players they can sneak on to their practice squad and potentially sign later.

Assuming Beathard will be on the 53-man roster by the time Week 1 rolls around, here’s a look at what the 49ers’ roster might look like:

QBs: 3 

IN: Jimmy Garoppolo, Nick Mullens, C.J. Beathard

OUT: Wilton Speight (practice squad)

RB: 4

IN: Tevin Coleman, Matt Breida, Raheem Mostert, Jerick McKinnon (IR-return designation, has to be on 53-man, could be put on IR the day after cutdown day)

OUT: Austin Walter, Jeff Wilson Jr.

• It seems cruel that Jeff Wilson Jr. wouldn’t make the roster and Jerick McKinnon would. That could certainly change, but it does not seem likely. McKinnon is expected to be back “soon,” according to general manager John Lynch on KNBR earlier this week, whatever that means. There is a possibility McKinnon is cut outright; while he would be due $5.7 million in guaranteed money this year, the 49ers are well under the salary cap, and he only has $4 million in guaranteed money remaining (split in each of the next two seasons), according to Over the Cap.
• Don’t bet on the 49ers to ditch McKinnon so quickly though; putting him on IR-return designation would create another roster spot and allow McKinnon eight weeks (eligible to play in Week 9) to fully recover from an ACL injury which he clearly still needs time to work back from. If they pick up an injury to any one of their other backs, McKinnon would essentially be a deferred investment who holds at least some of his initial value.

FB: 1

IN: Kyle Juszczyk

WR: 6

IN: Marquise Goodwin, Dante Pettis, Deebo Samuel, Jalen Hurd, Trent Taylor, Jordan Matthews

OUT: Richie James Jr., Kendrick Bourne, Malik Henry, Chris Thompson

• This one doesn’t get any easier to figure out. I badly want to put Richie James on this roster, but the numbers just don’t add up, and Shanahan’s glowing review of Matthews earlier this week, coupled with his consistent threat from the slot while the team does not really have another proven option there really makes it seem like he’s going to make this roster.
• It doesn’t feel like Trent Taylor’s going to get cut, and there’s been no indication the team will take seven wide receivers (with Beathard making the team it’s even more unlikely). However, Taylor’s Jones fracture in his toe and questionability to play early in the season does create a possibility for him to be cut, although unlikely.
• Bourne also received a pretty solid review earlier in camp from Shanahan, who said he’s had, like Matthews, “a hell of a camp.” While he is extraordinarily crafty, he’s inconsistent and drops the ball all too often. Still, it wouldn’t be surprising in the slightest if he made the roster.
• What’s worrisome is who will return kicks and punts if it’s not James. Dante Pettis was prolific in college but fumbled badly on a punt on Saturday (it’s still the preseason, but it’s also still a fumble). Deebo Samuel is an option, while D.J. Reed hasn’t looked dynamic at all. James is clearly the best returner on the team, but if he’s not going to make it, he could be a prime trade candidate for a team which needs receiving and returning depth.
• The other wild card here is Goodwin leaving in a trade. If cut or traded, the 49ers would only have to bear the remaining $1.2 million in bonuses split over the final two years of his deal, and he only has a $3 million guaranteed salary this season (for the 49ers to bear if he stays, or the trading team if he goes). Next year, that increases to $4 million, and the following year it’s $6.5 million, plus $31,250 for each game he’s on the roster, but that money is all non-guaranteed, according to Over the Cap. There’s no indication the team wants to part with Goodwin yet, and it’s unclear how great a market there is for him, but he could be enticing as a proven commodity for teams short on wide receiver depth (see: New York Giants).

• Trading Goodwin, of course, would leave a spot for James or Bourne to make the team (assuming neither is traded, it should be James).

TE: 3

IN: George Kittle, Ross Dwelley, Kaden Smith

OUT: Levine Toilolo, Daniel Helm, Tyree Mayfield

PUP: Garrett Celek

• This competition remains the same. Levine Toilolo’s shoulder inflammation hurt his chances, and Kaden Smith’s blocking bolstered his stock.

OL: 8

IN: Joe Staley, Laken Tomlinson, Weston Richburg, Mike Person, Mike McGlinchey, Justin Skule, Ben Garland, Najee Toran

OUT: Sam Young, Wesley Johnson, Joshua Garnett, Daniel Brunskill, Dillon Day, Willie Beavers, Ross Reynolds

IR: Shon Coleman – underwent surgery on fractured fibula, dislocated ankle

• It feels like the biggest question here is whether Skule or Sam Young make the roster as the swing tackle. The numbers with Beathard on the team don’t bode well for both making it and the question is whether Skule’s upside in combination with his performance thus far (penalties in first two games, none in third) is enough to outweigh the consistency of the veteran Young.
• Both, along with Najee Toran, spoke to KNBR earlier this week about their adjustments and what they’ve learned from the team’s offensive line veterans this preseason. All three took 27 snaps against the Chiefs, and Toran played left guard for the first time on Saturday. After allowing a bad sack on Nick Mullens, he improved, putting in the lead block for a Jeff Wilson touchdown run. Primarily a right guard, he’s also played some center and now left, which seems to be the 49ers testing his versatility.
• They also gave Daniel Brunskill a healthy a run at right guard with the starters (his 43 snaps led the team), and he looked solid, but had few reps preceding that. It’s unclear where he stands in the competition, but Toran would seem to have edge, having been healthy, generally good (although his Broncos game was poor).
• Joshua Garnett couldn’t make it into the game and received a pretty damning assessment from Shanahan when asked about him on Saturday. Said Shanahan when asked about Garnett: “It’s not just about ability and who’s the best. It’s about who’s going to be available. It’s not just our 53 for Week 1. It’s who’s going to the 53 we think can play with us throughout the year.”

DL: 10

IN: Dee Ford, Arik Armstead, DeForest Buckner, Nick Bosa, Solomon Thomas, Ronald Blair III, Sheldon Day, D.J. Jones, Kentavius Street, Damontre Moore

OUT: Jullian Taylor, Kevin Givens, Jamell Garcia-Williams, Jordan Thompson, Jay Bromley, Jeremiah Valoaga

• One question mark here is Ronald Blair III, who seemed pretty close to a lock to make the roster earlier in the offseason (and probably still remains that way) after being talked up repeatedly by defensive coordinator Robert Saleh.
• The issue is that Nick Bosa is 50/50 for Week 1 according to Lynch. Dee Ford is going to be back but won’t start practicing again until this week, and Blair has had a nagging groin issue. It may mean that Damontre Moore, an end who’s looked fantastic in the preseason, gets the nod over an interior defensive lineman like Jullian Taylor or Kevin Givens. Jeremiah Valoaga has also been solid, but Moore’s been with the team the whole offseason, and has been consistently good in all three games.

LB: 5

IN: Fred Warner, Kwon Alexander, Dre Greenlaw, David Mayo, Azeez Al-Shaair

OUT: Malcolm Smith, Elijah Lee, Mark Nzeocha, LaRoy Reynolds, Demetrius Flannigan-Fowles

• This number is a result of Beathard making the team. It would be six otherwise, and after/if a decision is made with McKinnon, there will likely be another addition here, for special teams if nothing else. Elijah Lee would get the nod over Al-Shaair here if he didn’t have surgery on his thumb. Availability and health makes a difference, as does age, and it feels more likely, at least right now, that Lee can be snuck onto the practice squad on cutdown day than Al-Shaair, whose rightfully got some buzz around him right now.
• Don’t rule out Smith, Nzeocha or Reynolds to beat out Mayo or Al-Shaair, but Smith’s struggles and injury history seem to indicate he’s not needed, while Reynolds (who’s had a tremendous preseason), for better and for worse, has a lot of miles on him, and Nzeocha, like Mayo, is a great special-teamer. The limited numbers here plus Lee’s injury makes the linebacker decisions much tougher than they would be if the 49ers went with two quarterbacks.

CB: 6

IN: Richard Sherman, Ahkello Witherspoon, Jason Verrett, D.J. Reed Jr., K’Waun Williams, Emmanuel Moseley

OUT: Tim Harris Jr., Dontae Johnson, Quinten Rollins

IR: Greg Mabin – sustained a serious calf injury on Wednesday

• If everyone in this group was healthy, there would be a real chance that the 49ers go five here, at least for cutdown day. But with Verrett and Williams huge question marks for Week 1, that seems unlikely. The wild card is Jimmie Ward, who played mostly at nickel corner in his 25 snaps on Saturday and looked natural and effective there, at one point covering off Tyreek Hill perfectly.
• There’s no real surprise in who’s making it, as Tim Harris Jr. just hasn’t performed well enough, and while Dontae Johnson has grown into the past two games late on, that means little when going against the second- and third-teamers especially after he’s had a poor camp preceding those games. Emmanuel Moseley had two PBUs on Saturday and has looked a very solid, promising depth option in his second year.

S: 4

IN: Jimmie Ward, Tarvarius Moore, Jaquiski Tartt, Marcell Harris

OUT: Adrian Colbert, Antone Exum Jr.

• Nothing changes here, and Colbert’s hamstring problem, which kept him out on Saturday, really put a dent into his remaining chance to make the team.

K/P/LS: 3

Robbie Gould, Mitch Wishnowsky, Colin Holba

• The only thing to note here is the 10-game suspension of long snapper Kyle Nelson (who has to sit 6 games this season), and whether he takes his starting job back from Holba at the conclusion of his suspension. The suspension oddly provides the 49ers with a free backup long snapper, but is only really useful if Holba is hurt in Week 8 (49ers have their bye in Week 3).