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You won't need to adjust the amount in Box 12a. Box 12 Code W shows all of your pretax contributions. For purposes of Form 8889, these are considered as contributions from your employer. Because all of these are pretax contributions, it is not necessary to separate how much you contributed personally versus how much was contributed by your employer.
If you had additional contributions with after-tax money, those would be reported separately as having been contributed by you, to calculate the deduction.
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