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You are correct Health insurance premiums are subject to FICA taxes and are NOT included into W2 boxes 3 and 5.
That amount is ONLY included into box 1 for employees who are also owners of S-corporation.
health insurance premiums are considered fringe benefits that an employer (S-corportaion) provides to you (an employee)
See following IRS publication
for specific conditions when Accident and Health Benefits may be excluded from wages;
and for special rules for 2% shareholder of an S corporation as an employee of the corporation for this purpose.
Specifically - see page 6 at the bottom
S corporation shareholders. Because you can't treat a 2% shareholder of an S corporation as an employee for this exclusion, you must include the value of accident or health benefits you provide to the employee inthe employee's wages subject to federal income tax withholding.However, you can exclude the value of these benefits (other than payments for specific injuries or illnesses) from the employee's wages subject to social security, Medicare, and FUTA taxes.
Thus consider your example - on your W2 form - you will have
in box 1 = $5000
box 3 = $4525 ($5000 minus $475)
box 5 = $4525
So your social security and Medicare taxes will be calculated based on $4525 while income taxes will be based on $5000.
And you are correct - for federal income tax purposes - you will deduct that amount $475 on form 1040 line 29 as an adjustment to income.