49ers' GM on Colin Kaepernick: QB could be back in '16

The San Francisco 49ers are not done with quarterback Colin Kaepernick, who was placed on injured reserve with an injury to his non-throwing (left) shoulder, ending his season.

At least that's the position of general manager Trent Baalke, who denied Sunday before the 49ers played the Seattle Seahawks that the move meant Kaepernick had played his last down in a 49ers uniform.

"I wouldn't say that at all," Baalke said Sunday in the press box at CenturyLink Field. "I think people are reading into that. For me, where we stand right now, I wouldn't read too much into that."

Blaine Gabbert started Sunday's game, his second since replacing Kaepernick atop the San Francisco depth chart. Gabbert won his first start, beating the Atlanta Falcons, but finances might be as great a factor as performance.

Kaepernick was 29th in passer rating (78.5) when he went to the bench. The 49ers can avoid paying his $11.9 million base salary if he is traded or release by April 1.

"Now is not the time to get into all the different particulars," Baalke said. "Right now he's no different than any other player that's been placed on IR. When that surgery takes place, then the rehab process, and get him ready for the offseason program is the next step."

Quarterback Dylan Thompson was promoted from the practice squad to the active roster to take Kaepernick's spot.

Just Friday, Kaepernick was listed as probable on the 49ers' injury report. Kaepernick said he was injured in the team's Oct. 4 loss to the Green Bay Packers.

Kaepernick played in nine games (eight starts) this season. He threw for 1,615 yards with six touchdowns and five interceptions. He also rushed for 256 yards with one touchdown.

The 49ers signed Thompson as an undrafted free agent out of South Carolina in May.