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If it wasn't so trendy for girls right now, it might have worked as a middle name for a boy. However, Nova is very feminine in use right now and increasingly gaining in popularity for girls, so I would leave it as a guilty pleasure for boys.

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Noah has similar sounds and is certainly a boy name. Do you like it as an alternative or is it too popular?
Neo on a boy has a similar vibe to Nova, but it is very wordy and Matrix associated.