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Form and 1099-R and qualified charitable distributions

I received a 1099-R which shows the following:
• Box 1: Gross distribution $xx,xxx.

• Box 2a: Taxable amount: $xx,xxx (the same as Box 1)
• Box 2b: The first box (Taxable amount is not determined) is checked with an “X”.
Here’s the problem and the question. A portion of the gross distribution represented “qualified charitable distributions” under Code Section 408(d)(8), made directly by the administrator of my IRA to qualifying charitable institutions. Because the values in Boxes 1 and 2a are the same, the income exclusion in the amount of the qualified charitable distributions appears to be lost. The entry in Box 2b contradicts Box 2a and otherwise does nothing.
What to do?