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Get your taxes done using TurboTax
"Does TurboTax have an offset for the amount of transfer that was sent to my church and is not taxable (NOT the whole IRA transfer went to charity?"
Yes.
Enter your 1099-R. Work through the subsequent screens until you see "About This Retirement Account" (you will see this only if you were 70 1/2 last year).
Answer "Yes, some or all of this withdrawal was an RMD".
This will expose a new line - answer whether part or all the the withdrawal was an RMD.
If you answered "part", then a new line will ask "how much applies to the RMD".
Then the next screen is titled: "Transfer to Charity?" Here you can indicate that part of the distribution was sent to charity. The dollar amount you enter will be treated as the QCD (qualified charitable distribution) and will be excluded from your taxable income in line 4b.
Remember that one of the benefits of the QCD is that it can count towards your RMD, which allows you to take the RMD and not pay tax on any part of it that was a QCD.
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