Are you sure that the QCD was not removed from your income? Look at lines 4a and 4b on your Form 1040. Is line 4b less than line 4a by the amount of the QCD? If so, your taxable income has been reduced by the QCD. The abbreviation QCD should also be to the left of the amount on line 4b.
If line 4b is equal to line 4a, after you entered the Form 1099-R did you continue through the questions in TurboTax? You should have come to a screen that asked if you transferred all or part of the IRA distribution to charity. Did you answer that you did, and then enter the amount of the QCD?
