Nope, never seen one. They are always present in mangas but are never the mc's.
There IS a shojo omegaverse manga called bite maker but it hasn't been translated yet
omegaverse used to be predominantly based in female fanfiction based in 1st person ( like harry styles x y/n or some shit) but it only really surfaced in manga form as yaoi as a more 'accepted' off-branch of the mpreg fetish
http://www.mangago.me/read-manga/kimi_no_koi_wa_watashi_no_koi_our_love/ by the way it's incest
So I got kinda interested in omegaverse, and as much as I love yaoi, I got curious: do you know any manga/Webtoon/thing in omegaverse where the MC is female? Could be fun to read for a change...