Question about damage calculation

[xerandus]

There are some gear mods like "Calefaction causes target to take +39% damage from Cold for 12 seconds", which are not modifying an ability of the character but is essentially modifying the mob itself. Where in the calculation is that bonus applied and how? Is it separate after all other calculations on the ability itself, including base damage? Is it essentially treated as a modifier to the mob's resists/vulnerabilities?

[Yaffy]

It's calculated with all other non-base damage percentage bonuses. So for example, if you used Calefaction with that mod and then used Ice Spear, it would be an equivalent to having a mod that says "Ice Spear does 39% more damage".
This is only the case after the last patch.

(Base damage+Flat damage) *Percentage boosts + (Base damage*base damage bonus-base damage)