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You probably have a retirement contribution in box 12 which lowers your box 1 income. But those amounts are still subject to social security and Medicare taxes.
The most common reason that Social Security wages reported in Box 3 of Form W-2 are greater than Wages, Tips, Other Income reported in Box 1 is due to pre-tax retirement plan contributions such as a 401(k) or 403(b). Also, if your employer's benefits include a Section 125 "Cafeteria Plan" the medical insurance premiums you pay are not included in Box 1, but are included in Box 3 and Box 5.
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