So the Human Variant in 5E D&D gets two different ability points, proficiency in one skill and a feat.
Let's say that human is a cleric with acolyte background. He takes a double dose of religion (Am I wrong in presuming you can do this?), then the proficiency in religion and then the "Skilled Feat" with one of the three skill as religion, can they stack and how?
You're either proficient with a skill/item/weapon and get to apply your proficiency bonus, or you're not; you can't be doubly or triply proficient in something. Some class features and special abilities may allow you to double your proficiency bonus in some situations, but these are always explicitly spelled out. As the PHB states on page 12, under the "Proficiency Bonus" heading:
Your proficiency bonus can't be added to a single die roll or other number more than once. Occasionally, your proficiency bonus might be modified (doubled or halved, for example) before you apply it. If a circumstance suggests that your proficiency bonus applies more than once to the same roll or that it should be multiplied more than once, you nevertheless add it only once, multiply it only once, and halve it only once.
And this is reiterated in further detail in the "Proficiency Bonus" section on page 173:
Your proficiency bonus can't be added to a single die roll or other number more than once. For example, if two different rules say you can add your proficiency bonus to a Wisdom saving throw, you nevertheless add the bonus only once when you make the save.
Occasionally, your proficiency bonus might be multiplied or divided (doubled or halved, for example) before you apply it. For example, the rogue's Expertise feature doubles the proficiency bonus for certain ability checks. If a circumstance suggests that your proficiency bonus applies more than once to the same roll, you still add it only once and multiply or divide it only once.
If you would be granted the same tool/skill proficiency by your background and your class during character generation, you get to just choose a different proficiency of the same type.
Extra: However, as mattdm's answer points out, Xanathar's Guide to Everything introduces a new feat, Prodigy, which amongst other things allows you to choose one skill you have proficiency in and double your proficiency bonus when using that skill - so as a variant human taking a feat at 1st level, you could improve your bonus to one skill in this way.
You can't, as explained at What happens if I get the same skill from both my background and my class? and in the Player's Handbook and Basic Rules.
However, there is a way to take a "double dose" of religion or any other skill as a variant human (or any other human, or a half-elf or half-orc). That is, you can take the Prodigy feat from Xanathar's Guide. This lets you choose an additional language, an additional tool proficiency, an an additional skill proficiency (following the same rules as above — no doubling yet). And it also lets you choose one skill you're proficient in and:
You gain expertise with that skill, which means your proficiency bonus is doubled for any ability check you make with it.
As a variant human, you can even take this at first level, instead of the Skilled feat. You don't need to "spend" the new skill proficiency granted by the feat on Religion, since you have it from your acolyte background — you can take something else. And then you can choose Religion as the skill for expertise.
If your character is human, half-elf, or half-orc, Prodigy is almost always a better choice than Skilled, especially if your DM is using the new rules for tool proficiency in Xanathar's. For example, if you have proficiency with Painter's Supplies, it's suggested that DMs consider giving you advantage and an additional benefit like extra information when examining religious artwork. In a party-based game like D&D, being really great at something is better than being middling-good at a bunch of things, and with 5E's "bounded accuracy" design, this kind of double-proficiency is hard to come by.
The rogue class has the Expertise feature, which basically does the same thing. But, you can't double these up for triple or quadruple expertise.
