Was the full amount included on 1040 line 4b? You can't change the 1099R. After you enter the 1099R it will ask if it was a QCD and how much. Are you taking your RMD? You have to be 70 1/2 to do a QCD. It won't reduce your AGI, it just won't be included in the AGI in the first place.
What code is in box 7 on the 1099R?
