When you make a Qualified Charitable Deduction (see topic at the bottom of this IRS web page) you get a 1099-R with the total distribution in box 1, and the box 2 "taxable amount" is reduced by the portion paid directly to the charity from the IRA. If all the RMD was paid to the charity, the box 2 amount should be zero.
On the line for the taxable amount, you enter "QCD". TurboTax will prompt you for whether any was donated to a charity, and complete your forms appropriately.
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