Colin Kaepernick's status with the 49ers remains in doubt despite new GM John Lynch's platitudes. (Stan Olszewski/Special to S.F. Examiner)

Colin Kaepernick's status with the 49ers remains in doubt despite new GM John Lynch's platitudes. (Stan Olszewski/Special to S.F. Examiner)

John Lynch continues to praise Colin Kaepernick while keeping options open

The 49ers have a new general manager, head coach and waiting game for how they’ll fill the quarterback position.

A lot of that is because Colin Kaepernick — the best QB currently on the roster by no insignificant margin — can release himself of his contract between March 2-7, the league’s opt-out period. Or, he’ll keep his deal and the Niners would then weigh whether he’s worth the $14.5 million of base salary he’d be owed for next season.

There’s room for negotiation between those two extremes that could keep Kaepernick in Santa Clara for a discounted rate, should he find his value in the open market isn’t what he was hoping.

John Lynch, the 49ers GM, has struck positive notes about Kaepernick since taking over the role earlier this month.

“Every time we talk about Kap, I think about the guy that was in the Super Bowl — that wasn’t too far away,” he said on 95.7 The Game on Tuesday. “I remember that team, and I remember broadcasting and sitting down and being impressed with that young man.”

Kaepernick reached out to Lynch after the former safety accepted the position, replacing Trent Baalke, whose relationship with the franchise quarterback was hardly friendly.

Working with a GM he has some respect for would likely be a welcome departure for Kaepernick.

“I think there was a trust there,” Lynch said earlier this month, recalling meetings he had with Kaepernick while a broadcaster. “I think that trusts extends and I was thrilled when he reached out. And I’m looking forward to talking to him.”

Despite the platitudes from his new bosses, the position is far from Kaepernick’s. Lynch said he and Kyle Shanahan are considering every option in terms of filling that role.

First, they’ll work with Kaepernick while both sides determine how — if, at all — they want to work together in the future.

“We’ll be up front with what we’re thinking and we want to know what he’s thinking too,” Lynch said.

ESPN reported during the lead up to the Super Bowl that Kaepernick would opt out of his contract when it’s a possibility. And most of his actions last year — from restructuring his contract to selling his San Jose mansion — would indicate he has intentions of leaving the organization. But, he was also careful to compliment CEO Jed York and executive Paraag Marathe after the 49ers lost to the Seattle Seahawks to conclude the 2016 season.

“I have a great appreciation for this organization,” Kaepernick said. “Jed and Paraag, I have a good relationship with them. So, a lot of things to think about moving forward and we’ll see where this goes.”Colin Kaepernickjohn lynchkyle shanahanNFLSan Francisco 49ers

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