Apart from the price modification feature, you can also set a fixed price for a variation:
If you want to set the main product price to zero or leave it empty, use the = option for the variation price modification type.
It will set a fixed price for the variation. If you put multiple variations as ‘=’, the final price will be a sum of all the options.
If you set the first variation price modification to ‘=’, it will overwrite the main price, but the subsequent variations will add to the main price.