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Yes there's Jerusalem as city state in Civ 6 and also Judaism as a religion in many of the games (I think in every one that has religion as a mechanic). Tbh I can undestand if they conciously decided to not include Jews as civilization in the game. Of course they would make them look normal and whatnot but with how touchy some people are there's still risk of it exploding for some stupid reason and the damage control for that would be more expensive than if it was some other civ.