Yes, the 1099-R includes a Qualified Charitable Distribution in both box 1, gross distribution, and box 2a, taxable amount. The adjustment to the taxable amount is made on your tax return. There is no indication on the 1099-R that you made a Qualified Charitable Distribution. When you enter the 1099-R in TurboTax, it will ask whether you transferred any of the distribution to charity, and it will make the appropriate adjustment on line 4b of your Form 1040.
