Your can setup specific Pricing Rule for a product variant.

Navigate to 'Pricing Rules' section on the product management page.

Add Pricing Rule

  1. To add a new pricing rule for a variant, select 'Create new pricing rule'.
  2. Let says, we want all hats in Red to be sold for $39, which is $10 more then default price.
  3. Navigate to 'Rules' section and choose variant.  In our case, we will configure various sizes for Color Red. 

Pricing Rule List for Variants

Once we added a new pricing rule for each variant of red, in different sizes: small, medium and large, we have a complete list of variant pricing.