This phrase may date back to 1949, where it appeared in an a Nebraska State Journal article by J.E. Lawrence; however, it resurfaces from time to time, like herpes, from a 2001 film by Billy Frolick to a 2017 Europop album by Johnny Logan.
A thousand Americans are dying of COVID-19 every day; it’s true. And you have —it is what it is.
A) A phrase that seems to simply state the obvious but actually implies helplessness.
B) A phrase that seems to simply state the obvious but actually means "it will be what it is," as in "it ain't gonna change, so deal with it or don't." See also tough shit, oh well, cry me a river and tfb.