The Adjusted Gross Income (AGI) is calculated before charitable contributions are taken into account.
When you look at Form 1040, the AGI is reported on line 11. This number is then adjusted by the itemized deductions, standard deduction, or standard deduction plus Cares Act charitable contributions along with the Qualified Business Income (QBI) deduction (if applicable) to determine the taxable income shown on line 15.
If you still feel there is a mathematical issue, please provide a few more details.
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