I assume you are referring to the question that comes up immediately after you enter the 1099-R. The question is Is the IRA/SEP/SIMPLE box on this 1099-R checked?
This question verifies the entry you made on the previous screen. It also may change the line on which your retirement distribution appears.
If the IRA box is not checked, your distribution will appear on line 5 of your 1040. If the IRA box is checked your distribution will appear on line 4.
You can check your tax return and your 1099-R to make sure your distribution is on the right line.
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