After you entered the 1099R TurboTax will ask you if any portion of your distribution was transferred to charity (if you are over 70 1/2). You can then enter the amount transferred to charity.
For a QCD, check 1040 line 4b. It should be 0 (unless you have other taxable 1099Rs) and the QCD box checked. The code in box 7 of form 1099-R must be 7 and the box IRA/SEP/SIMPLE must be checked. You can’t do a QCD from a 401K.
If you are looking at a summary screen or review screen those show the full amount as income and lump a lot of stuff together. You need to check the actual 1040 form and make sure it's right. Check lines 4b & 5b for any taxable amounts.
