All three of my names (and my maiden name too, come to think of it) have at least 2 acceptable spellings and my first name has about 8. I think I would try to avoid names with that many variants, and especially avoid choosing one of the less common variants.
Thanks everyone Zayne isn't a made up spelling, according to name books it's the Hebrew spelling opposed to the Muslim or English (we are British Christian/ Gambian Muslim but just preferred that spelling)
We might go for the more common spelling though... poor kid will always be spelling his surname as it is!
With the up-rise in social media, his peers, associates and work colleagues will know exactly how his name is spelled. It'll just be clarifying the spelling on forms which won't be too much of a strain.