Enter the 1099-R exactly as you received it. After you have entered all of your forms 1099-R you will have a series of follow-up questions. One will ask if you have made any qualified charitable donations ("QCD") - this is where you will tell TurboTax about the donation you made and it will then be excluded from your income with a notation on Line 4 of Form 1040 of "QCD".
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