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Why Kyle Shanahan kept C.J. Beathard on the bench until Sunday

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Without a horrendous call on wide receiver Pierre Gascon with only seconds left in a two-point game, rookie C.J. Beathard would have led the 49ers past a playoff caliber team at home. In the process he would have erased a 17-point Washington advantage at FedEx Field. Immediately, Beathard would have been part of Bay Area sports lore, no matter what he did for the rest of his career.

Instead, the 49ers lost their fifth straight game by three points or fewer, the first time that has ever happened in NFL history. The team was left to stew after their sixth straight loss to start the season and left to wonder why referees called Gascon for a “pick” play when the pass was intended for him.

However, a bigger story loomed; Beathard supplanted the struggling Brian Hoyer as the starting quarterback. Beathard threw for 245 yards, and a 45-yard touchdown pass to Aldrick Robinson after subbing for Hoyer, who completed 4 of 11 passes for 34 yards

While Hoyer was thoroughly ineffective, Beathard’s performance was ragged, gutty and refeshing, something Beathard was known for during his days at Iowa.

It makes you wonder if the 49ers should have inserted Beathard earlier in the season. Now at 0-6, the season is all but lost.

The answer to that question depends on how much you trust 49ers coach Kyle Shanahan. As of a few weeks ago, Shanahan said he wasn’t even considering Beathard as the starter, despite Hoyer wallowing near the bottom of the league in most passing categories.

Shanahan changed attitude towards Beathard this week, saying every position is under review and most crucially, that Beathard improved his practice play.

The feeling was Beathard wasn’t ready until now and that injecting him into a game any earlier could have destroyed his confidence.

But what was abundantly clear through training camp and the off-season program? Hoyer was undeniably the best quarterback. Towards the end of training camp, the offense clicked, with Hoyer consistently zipping passes to receivers before they made their breaks. The offense looked smooth and maybe it took this long for Shanahan to realize that Hoyer couldn’t transfer his practice play to the game.

It didn’t help that Hoyer would show flashes once the season started. In the last game, his first and fourth quarters were brilliant and his arm strength was clearly evident in those moments.

But what Hoyer failed to do at any moment was make the great play. He never evaded the on-rushing player, peer down field and then uncork a pass to a waiting receiver.

It took Beathard just a few drives to do exactly that. He wriggled out of the pocket in the fourth quarter and found Aldrick Robinson for an electrifying 45-yard catch-and-run touchdown. The play cut the lead to 26-24. More importantly, it signaled who Beathard is.

“Hearing him in the huddle is awesome,” tight end George Kittle told NBC Bay Area. “Cool and ca;m, awesome to see him on the field. He does what he always does, he made some guys miss,chucking balls, he’s just a play maker. He showed up today and he’s going to keep showing that every time he plays.”

Kittle knows better than anybody; he was Beathard’s roommate at Iowa.

Other players backed up what Kittle observed. Running back Carlos Hyde said Beathard was “cool, calm and collected.”

Looking backward to wonder what might have been, might not be that valuable. However, the future could be bright as Beathard prepares for the visiting Cowboys while practicing with the first team. That means making throws to first-string receivers Pierre Garcon, Marquise Goodwin and even Hyde.

With a greater handle on the offense and practice time with the starters, Beathard could give the 49ers the edge needed to turn close losses into satisfying victories. Whether he could have done that earlier in the season is basically an exercise in futility.