We know that Tom was not one of the following: Man, Elf, Dwarf, Hobbit, Orc, Troll, Ent, Vala, Eru, etc. etc.
We are left with only two reasonable suggestions for Tom's origins: he can be either a Maia or something which Tolkien never mentioned elsewhere. I believe in the latter alternative, but I can certainly see why some people like to think of him as a Maia.
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