It actually doesn't get included in the AGI since it is backed out. It is added and included and then backed out because it needs to be reported to the IRS since it is on the W-2 AND for those people who can also claim the Earned Income Tax Credit or Additional Child Tax Credit, the numbers need to be added in so they can be counted.
But in the end, the numbers that you entered from box 12 code II that went onto line 1d are not included in your AGI. Any numbers you entered from box 1 are included in your AGI.
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