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thanks Mike,

 

Based on your example, it seems the net additional owed can be calculated by math below:

 

$250000 * 1.45% + (Sum_of_all_Box_5_on_W2 - $250000) * 2.35% - Sum_of_all_Box_6_on_W2

 

Which calculated that I owe only less than $1000, but turbotax somehow tells me I owe another $3k, so still there is a gap.