Lynch thinks Garoppolo-to-Lance transition will play itself out

There will come a time when Trey Lance takes over permanently as the 49ers’ starting quarterback.

But when?

The master plan, according to 49ers general manager John Lynch, is flexible. He says the time will come when the time comes.

“That will play itself out,” Lynch told NBC Sports Bay Area. “I really believe that.”

The 49ers traded up to No. 3 overall on March 26 and, one month later, selected Lance to be the team’s quarterback of the future.

Veteran Jimmy Garoppolo remained as the starter through the offseason program, training camp and the first four games of the regular season.

Lance got his first NFL start when Garoppolo could not play in Week 5 against the Arizona Cardinals due to a right calf injury.

Now, the 49ers plan to turn back to Garoppolo after the bye week to face the Indianapolis Colts on Sunday.

Coach Kyle Shanahan had already said nothing changed, as far as Garoppolo remaining the starter, even before Lance was diagnosed with a left knee sprain one day after his first complete NFL game. Lynch said he and Shanahan communicate regularly, and he said he believes the 49ers are in a good spot with their quarterbacks.

“You have to step back and say, ‘For the immediate future what’s our best opportunity?’ ” Lynch said. “And let’s also think about the reality of the future. How do we continue to best develop Trey for the long term?

“You got to keep the absolute near future in mind, and you also have to keep the big picture in mind. But nothing is more important than finding a way to beat the Colts when we line up coming off this bye, and we’ll have that in mind.”

Lance completed 15 of 29 passes for 192 yards with no touchdowns and one interception in the 49ers’ 17-10 loss to the Cardinals before the bye. He also rushed 16 times for 89 yards.

Lynch said the Cardinals’ defensive scheme made a “concerted effort” to stop Lance.

“I think that tells you what they thought of him,” Lynch said. “He’s got that competitive greatness, where the moment is not too big for him.

“At the same time, you saw things like operation time. How quickly the plays get in. It took a little longer.  But that’s going to come with reps. At some point, yes, you have to go through that.”

Lance’s agility, athleticism and running ability factored into the reasons the 49ers selected him to eventually take over as the team’s quarterback.

But how much running is too much running?

“We all talk about that,” Lynch said. “Trey does a very good job of protecting himself. Now, sometimes that’s out of your control. Those weren’t all designed runs — flushed from the pocket or make a decision to run.

“I think he makes very good decisions. You got to trust him. Of course, you’re always going to try to protect your players and we’ll continue to do that. But I think he does, for the most part, a very good job of being very cognizant of getting what he can get and, then, protecting himself.”

Garoppolo completed 66.1 percent of his passing attempts before the injury sidelined him. He threw for 925 yards in 3 1/2 games with five touchdowns, two interceptions and a passer rating of 96.9.

The 49ers believe they are in a better situation this season with Lance stepping into the backup role that Nick Mullens and C.J. Beathard held in the past.

“We have good options, and that’s what we’ve been striving for, to have a real strong quarterback room,” Lynch said. “We know that we have that. Jimmy’s on a good trajectory to be ready for Indy.

“We’ll continue to make decisions that give us the best opportunity as an organization to win football games.”

RELATED: 49ers overreactions: What to make of Lance's designed runs

The 49ers emerge from the bye week on a three-game losing streak. With 12 games remaining in the regular season, the 49ers (2-3) must start winning to be in position late in the season to contend for a playoff spot.

“We really believe this team still has a shot at all of our aspirations,” Lynch said. “We would never fall short of that, in terms of throwing whoever it is at that position, such a critical position, whoever gives us that best opportunity.

“We’ll continue to make those decisions but I think the future is bright for Trey. (We) saw a lot of encouraging things. I think he’s doing well. I think there’s also so much room for growth and, I think, reason to be optimistic that growth is going to come.”

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