All skills have a base amount of damage that they would deal without any stats, which is called base damage. Base damage can only be modified by a skill’s tree.
The default base damage for each skill is listed on its tooltip.
Melee skills typically have 2 base damage total because most of their damage comes from weapons.
Spells and throwing attacks can have much more base damage, but the exact amount varies a lot between skills.
When calculating damage dealt, stats like "+5 melee fire damage" are multiplied by the skill’s added damage effectiveness, then added to the base damage before stats like "30% increased damage" and "10% more damage" are applied.
Added damage without a damage type, such +5 Melee Damage, adds damage of a type that depends on the base damage type of the skill. For example +5 Melee Damage will add 5 Melee Physical Damage to a Physical Melee Attack but 5 Melee Fire Damage to a Fire Melee Attack.