49ers GM John Lynch raves about draft’s QB class

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INDIANAPOLIS — The 49ers have the No. 2 pick in the 2017 draft, but they won’t use it on their biggest area of need because this year’s quarterback class is weak and …

Wait. What? Hold on.

General manager John Lynch spent much of Thursday at the NFL combine dumping cold water on what has become nearly gospel. Weak? Lynch suggested he was wowed by this year’s QB class.

He said Notre Dame’s DeShone Kizer “blew the doors off” his interview with the 49ers on Wednesday night, Clemson’s Deshaun Watson has a “confidence” and “aura” that’s “pretty special” and the more he saw of North Carolina’s Mitch Trubisky, the more he liked him. As for Texas Tech’s Patrick Mahomes, Lynch offered that “the film’s pretty special.”

“I think it’s a very talented draft class at that position, one we’re very excited about,” Lynch said. “And, look, I don’t think you need to be too transparent to realize that’s a position we’re looking at. We don’t have any (QBs). That’s a position that’s a big focal point of our preparation right now and this week’s a big part of that.”

It’s possible Lynch is being sincere, but even rookie GMs are fully capable of creating predraft smokescreens.

Lynch has also said the 49ers are open to trading the No. 2 pick, but he won’t maximize the value of the selection if it appears he’s too eager to move back in the draft. So perhaps his generous appraisal of the 2017 QBs is meant to signal the 49ers won’t trade the No. 2 without receiving a nice haul in return.

Yes, lying season in the NFL can get confusing, but there’s no doubt Lynch was truthful when he said this: The 49ers need quarterbacks.

DeShone Kizer. DeShone Kizer. Photo: Lisa Blumenfeld, Getty Images Photo: Lisa Blumenfeld, Getty Images Image 1 of / 1 Caption Close 49ers GM John Lynch raves about draft’s QB class 1 / 1 Back to Gallery

Barring the unforeseen, they will have zero on their roster when free agency opens Thursday.

The unique situation explains why both Lynch and head coach Kyle Shanahan have refused to dismiss the possibility of Colin Kaepernick re-signing with the 49ers after he officially opts out of the final year of his contract before free agency.

“There are things that Kyle likes about his game,” Lynch said. “I think it would be foolish to say we’re done with this.”

Despite their 2-14 record last season, the 49ers’ head-coach and GM openings were viewed as attractive by many largely because the new hires would have a clean slate to rebuild as they saw fit.

And nowhere is that more evident than at the most important position in the NFL.

“A lot of people look at it like ‘Oh my gosh, you don’t have any quarterbacks,’” Lynch said. “But that also is somewhat liberating in that you can create this thing in that position that is so critical in the way that you want it. Now, we’re restricted by who’s available, but I think we’ve got a lot of great options at our disposal. We’ve got the No. 2 pick in the draft.”

Before the 49ers use their first draft pick, however, their most pressing needs will come into sharper focus after they wade through free agency. Last year, they took their conservative approach to free agency to the extreme under GM Trent Baalke. They signed only guard Zane Beadles and third-string quarterback Thad Lewis.

On Thursday, Lynch smiled when he was told 49ers fans have been conditioned to a nap during the first day of free agency. His advice next Thursday?

“Stay awake,” he said. “We need players. We’ve got to get ourselves in a situation … so that we don’t go into this draft saying we have to have this. Everyone says the best way is to go in and (draft) the best players, but sometimes you can’t do that. You need certain positions. And we don’t want to be in that position everywhere.”

Eric Branch is a San Francisco Chronicle staff writer. Email: ebranch@sfchronicle.com Twitter: @Eric_Branch