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Master Set refers to the number of unique cards in a set, including different rarities, or in the case of Structure Decks, the amount of cards in the set including repeated cards.
Example Set: 60 cards
Additional Rarities of Cards above (assume all to be unique)
The Official Set Designation is 60 Cards. However, if the Additional rarities were to be included in the count, the Master Set count would be 106.