Your W-2 typically does not show your gross wages, and it does not show the net wages that you actually received. The wage amounts in boxes 1, 3, and 5 are amounts subject to taxation for various purposes. Each amount is a portion of your gross pay, calculated according to the rules for a particular tax, but they are not different wages. They are just different views of the same total wages.

For example, depending on various benefit options offered by your employer, if your nominal gross pay is $125,000 you might see $116,000 in box 1, $118,500 in box 3, and $125,000 in box 5, and the amounts in your actual paychecks might add up to $100,000. The $116,000 in box 1 is part of the $125,000 gross, the $118,500 in box 3 is part of the same $125,000 gross, and the $125,000 in box 5 is the entire $125,000 gross, but it's all the same $125,000. Of that gross amount, $116,000 is subject to income tax, $118,500 is subject to Social Security tax, and $125,000 is subject to Medicare tax. But they are not different wages. They are different portions of the same $125,000 gross wages.

The Social Security and Medicare taxes in boxes 4 and 6 come out of your gross wages. They are part of what makes your net wages, or "take home pay," less than your gross wages.