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Is the discrepancy (at least partially) due to a difference between cash basis and accrual basis accounting? AF reports can be run on a "trade date" or "payroll data" basis. Check the top of the report to see which one you have and then run the other to see if that takes care of your problem.

If there were a minimum amount of wages needed for FICA withholding, it would surely be well below $50,000! There may be some exceptions for students (but that would probably be inconsistent with there having been $50,000 reportable income) or for certain kinds of non-covered governmental work (i.e., if the employer is a governmental entity not participating in Social Security). Would either of those apply? Otherwise, how could someone earn $50,000 and not pay FICA taxes?

I have never seen a w-2 with income that did not have withholding for taxes and FICA. I don't think there is a minimum amt of w-2 wages needed for FICA withholding.

I would go back to client and ask them.