Kami-sama wa Chotto dake Ijiwaru

One day the ordinary beta, Nao, reunites with Nagi, an old alpha friend that moved away long ago. This handsome, perfect, princely alpha Nagi has never forgotten the "vow" they exchanged, even as he grew up. And so we find Nao, whose heart races as he finds himself passionately embraced. However, right in the middle of enjoying this reunion, Nao's body goes through a heat that no beta should experience. It's an indication that his secondary gender, despite the one in tens of thousands odds, has changed...
(Source: Overlap, translated)