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Side soreness, precaution and a fairly well-rested Yankees bullpen resulted in Clarke Schmidt’s being scratched from his scheduled start Saturday.

The righty said he felt “a little extra soreness” in his left side in his most recent outing — when he built up to 90 pitches for the first time in a win over the Blue Jays on Sunday — and it lingered during his throw days during the week. The discomfort was serious enough to warrant a Friday afternoon MRI exam, which came back clean.

Schmidt left the Stadium that night believing he would get the ball the following day, but Max Fried’s seven strong innings Friday, which followed an off day Thursday, helped convince the Yankees to start Ryan Yarbrough instead in what amounted to a bullpen game.

The Yankees believe Schmidt will re-enter the rotation Tuesday against the Padres, and Schmidt himself said he is “fine.”

But with a starting group that has lost Gerrit Cole for the season, Luis Gil for months and Marcus Stroman for at least weeks — and contains struggling options in Carlos Carrasco and Will Warren — any reason for precaution is a concern.

Manager Aaron Boone acknowledged the precarious state of the rotation “factored in” to erring on the side of caution.

“But at the same time, we’re going to try and do what’s right for [Schmidt],” the manager said before Yarbrough was strong (four one-hit, one-run innings) in a 3-2 loss to the Rays. “Obviously these guys go out there and pitch through things throughout, but there’s definitely a little bit of that caution involved here, too.”

Schmidt has not been a model of health, a lat strain limiting him to 16 starts last season before a few setbacks in spring training — first a minor back issue and later right rotator cuff tendinitis — forced him to start this season on the IL because he was not fully stretched out.

The 29-year-old, who has pitched to a 5.52 ERA in his three starts, said the side issue was unrelated to his shoulder.

“It just kind of happens, sometimes game to game and as your pitch [count] continues to build,” Schmidt said about the possible source of the soreness. “As your workload builds, more stress.

“But yeah, I feel confident and comfortable with where I’m at.”

The Yankees felt better about where he was at following the MRI exam that showed no damage.

“It was definitely a relief,” Boone said. “We should be OK moving forward.”