When will 49ers’ Harbaugh draft QB?

It’s a gut-instinct call, and it will be all Jim Harbaugh’s to make next week.

No big deal. Only the future of the franchise at stake here.

Obviously, the 49ers desperately need a quarterback (or two), even if Alex Smith chooses to come back for a seventh season.

And Harbaugh is

an esteemed evaluator of that position, which is a large reason why the 49ers gave him $25 million to be their coach.

In other words, the first enormous Harbaugh moment has arrived.

The NFL Draft starts Thursday April 28, the 49ers have the seventh overall pick, and there are two or three intriguing prospects who may be worthy of that selection.

But if you interpret the signs and intimations from Harbaugh and general manager Trent Baalke on Wednesday, it seems likelier and likelier that the 49ers will not be using the No. 7 pick on a QB.

The top-rated QB is Auburn’s Cam Newton, who probably will be gone by the 49ers’ pick (and might not be their ideal choice, anyway).

And Missouri’s Blaine Gabbert, the other QB projected to go in the first pod of picks, is an interesting choice but probably not more valuable to the 49ers than one of the elite defensive players.

I think the 49ers will take LSU cornerback Patrick Peterson, Nebraska cornerback Prince Amukumara or North Carolina pass rusher Robert Quinn or they will trade down. And they will get their hand-picked Harbaugh QB at a later point.

It’s just an interpretation, of course.

Baalke and Harbaugh both were determinedly indirect on all draft questions and Baalke continued to push the idea that Alex Smith’s return was a natural possibility.

But Baalke was clearly less effusive about Smith than Harbaugh has been all offseason, and my suspicion all along is that Harbaugh considers Smith his fallback option.

Which leads us back to the draft, the 49ers’ first pick, and the sense that they do not feel the need to burn it on a QB.

It’s about the gut feel. And Harbaugh being the right guy to sort through the second- or third-tier candidates — as Bill Walsh did when he picked a guy named Joe Montana in the third round.

“There’s things to playing the quarterback position — it’s the DNA of quarterbacks,” Harbaugh said Wednesday afternoon. “They have it or they don’t.”

Harbaugh has great confidence that he can divine the difference. And if you’re not 100-percent sure of that with Newton or Gabbert, then the 49ers have to trust Harbaugh to find it elsewhere.

My guess is that the 49ers are focusing on potential second-round options such as Florida State’s Christian Ponder or TCU’s Andy Dalton.

Neither QB is as athletic or strong-armed as Newton or Gabbert, but both could better fit the West Coast offense that Harbaugh will run with the 49ers.

The West Coast, of course, puts a higher value on accuracy and poise than deep throwing.

Or the 49ers could trade out of the seventh slot with a team that wants to move up for Gabbert (if he’s still there), and maybe take Washington’s Jake Locker 10 to 15 picks later.

One highly-rated QB I feel confident the 49ers will not select: Arkansas’ Ryan Mallett, who is not nearly athletic enough to flourish in the West Coast offense.

“With Jim, he’s got a lot of intuition about him when he looks at the quarterback position,” Baalke said of Harbaugh. “He’s been very successful in not only picking them but also in developing them.

“So that definitely plays into it from my perspective. I like to just listen to what he says and why he likes a particular trait in a quarterback.”

Don’t underestimate Harbaugh’s belief that he can mold a QB into something greater than others perceive is possible.

Andrew Luck was not considered a superstar prospect out of high school — Harbaugh saw otherwise, and that did not turn out poorly for Stanford, Luck or Harbaugh.

There could and probably should be a QB who reminds Harbaugh of Luck in this draft, and I don’t think that’s Newton or Gabbert.

That QB should be available in the second or third round, which the 49ers probably already have deduced.

Or else the 49ers could totally flub this draft, end up with the first overall pick in 2012 and then just take Luck.

That wouldn’t take too much analysis or gut instinct. That would just be accidentally brilliant.