Magic Attack does not apply. The only contributing factor is the base damage of the spell itself (equal to the rank of Mana Crystalization), multiplied by the skill's coefficient. Additionally, the skill cannot deal critical damage.
Example:
Mana Crystalization is Rank 1.
All other skills are Rank F.
The skill will deal 2400 base Fireball damage, multiplied by the Rank 1 damage coefficient of 0.8.
This results in a maximum damage output of 1,920 damage.
That is the highest this skill will ever hit.
No alchemy bonuses apply.
Reforges do not apply to the skills.
Ice Spear damage does not decrease as it chains but is capped at 16 chains. Unfortunately, the skill's damage is so low that it won't matter all that much.