General manager John Lynch discussed with coach Kyle Shanahan a few weeks ago the possibility of Jimmy Garoppolo remaining with the San Francisco 49ers, but as a backup quarterback.

Shanahan then talked to Garoppolo, but didn’t think he was going to work out.

“It seemed like there was little chance of that happening,” Shanahan acknowledged Tuesday. “I remember the first day of training camp when I said to Jimmy, ‘Hey, if you don’t like any of the opportunities, if you don’t go where you want to go, if you don’t get the contract you want, we want to have you here as a backup.’ .

When the preseason ended without another chance, that’s what happened. Garoppolo agreed to stay with San Francisco at a lower salary.

And the quarterback who helped the Niners reach the NFC finals twice in the past three seasons will back up Trey Lance, who hasn’t been tested.

“We always made it clear to Jimmy the maximum salary and that he would be a backup supporting Trey, if that was okay with him. That was obvious to us,” Shanahan said.

Instead of the $24.2 million non-guaranteed base salary Garoppolo was owed this season, he will receive a guaranteed $6.5 million base salary, as well as a $500,000 roster bonus and the opportunity to receive an extra 9 million in bonuses for playing.

The deal includes a no-trade clause and prevents San Francisco from putting the franchise tag on him at the end of the season.

Although it represents a sizable pay cut from what Garoppolo was owed in his original deal, it is possibly more than he would have received as a backup on the open market and provides the Niners with a proven backup in case Lance is injured or has a problem. difficulties in its first season.

“They were going to exhaust all their opportunities,” Lynch said of Garoppolo’s representatives. “They waited until the end. We wait for the end. But I had been in communication and it paid off yesterday morning and we nailed it down shortly after practice was over.”

Garoppolo will return to the daily activities of the 49ers after not attending a meeting since he finished last season. He has only thrown off the field during practice.

Shanahan acknowledged that after five years in the system, Garoppolo should have no problem getting ready before the season starts on Sept. 11 in Chicago.

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