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I entered my IRA contribution from box 12 when entering my W2, then when I get to the "deductions" part of the process it asks what amount I contributed to my IRA. Do I enter the same amount from box 12 again?
No, do not enter this information twice. If you have a SIMPLE-IRA through your employer, it will be reported with code S in box 12 of your W-2. You should only enter this information in the W-2 section of TurboTax. The question in the IRA section is referring to IRAs that you set up yourself, for example, at your local bank. Contributions to this type of IRA are not reported on a W-2.
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