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You have to reduce the Net Profit by the deduction allowed for one-half of your self-employment taxes.
So check 1040 Schedule 1 line 15. You have to deduct that amount from your Schedule C Net Profit. That will give you the allowed contribution for self employment & 1099NEC income.
The calculation for a self-employed person for a SEP IRA contribution is different than the straight 25% of net income.
Per the IRS:
To calculate your plan compensation, you reduce your net earnings from self-employment by:
You use your plan compensation to calculate the amount of your own contribution/deduction. Note that your plan compensation and the amount of your own plan contribution/deduction depend on each other - to compute one, you need the other (this is a circular calculation). One way to do this is to use a reduced plan contribution rate. You can use the Table and Worksheets for the Self-Employed (Publication 560) to find the reduced plan contribution rate to calculate the plan contribution and deduction for yourself.
For a self-employed individual, the maximum contribution is 20% of net earnings, not 25%, because the SEP contribution itself effectively reduces the compensation on which the base rate of 25% is being applied.
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