I know that it is a Mitzvah Deorayta and in the 613 Mitzvot, it is reported as a Mitzvat Asse... But according to Yalkout Yossef and the Siddur Tefilah Chazon Ovadia with Rav Ovadia Yossef’s Hashgaha it is not allowed to mention the wording "Mitzvat Asse" in the Leshem Yichud which precedes the Beracha. If it’s a matter that we don’t have Beit Hamikdash today then please explain the relationship between Beit Hamikdash and the Sefirat HaOmer.
There is a dispute among classical sources (Rishonim). According to the majority, counting the Omer is dependent on the Omer offering on the second day of Pesach and the “2 loaves” offering on Shavuot (as it appears from a simple reading of the verses in VaYikra 23), in which case today the Mitzvah today is Rabbinic, as the offerings are not in practice. According to another opinion, the obligation is independent of the actual offerings and is only connected to the dates of the offerings, in which case the counting today would be of Torah status. In either case counting is one of the 613 commandments, many of which do not apply while the temple is not standing (may it speedily be rebuilt!) Rav Ovadia Yosef’s position is that Sefirah today is rabbinic. This is the commonly accepted ruling.