It does not matter that they were your (employee) contributions, if Box 5 on your 1099-R is for health insurance, you should answer "yes" to the question that follows asking if the amount in Box 5 is for Health Insurance Premiums and enter the full amount.
Box 5 could also report Roth IRA Contributions.
If the amount in Box 5 on your 1099-R (Civil Service or other) is NOT reporting Roth contributions, it is ONLY reporting Insurance payments, so in that case, enter the full amount as insurance.
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