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As a learner of English I know that yes is a standard variant and the other two are informal, spoken words. I know nothing more about it, and always try using the yes variant, just to not sound inappropriate. But I'd like to be able to not sound too formal in a casual conversation.

Could you help me understand the differences between these words and the contexts in which it is okay to use them?

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    There is a combination "yeah, right" but it is not the same with "yes, right" – GEdgar Jul 10 '11 at 16:42
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You are correct that "yeah" and "yep" are informal variants of "yes." In conversation among friends, any form is appropriate, but "yep" has a slightly dismissive tone.

"Did you find your wallet?"

"Yeah, I left it in the other room."

As opposed to

"Did you get directions to the theater?"

"Yep."

In the second example, you're implying that you've already got directions and you don't need to spend time hearing them again.

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    "Yeah" can also be used as a cheer or exclamation. – Maxpm Jan 14 '11 at 2:23
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    I agree. "Yep" can often express impatience, though not always. – Noldorin Jan 16 '11 at 19:08
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    You should compare "Yeah, I left it in the other room." with "Yep, I left it in the other room." Obviously the second sentence sounds more abrupt in your example since its only one word... – Pacerier Nov 8 '13 at 13:35
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    I disagree that "yep" has a dismissive tone. While I agree that if I'm being dismissive I'm more likely to use "yep," I'm also highly likely to use the word when I'm NOT being dismissive. Its use is not a good indicator of whether the speaker is being dismissive. A response consisting SOLELY of the word "yep" might be. – Darryl Oct 24 '16 at 17:54
  • I don't think this is accurate. You can say "yeah right" and that's dismissive but you can't say "yep right". I think you really have to consider the tone. I think it's too complicated to actually find rules for these things, it's more of a feeling you slowly develop the more you hear these words. – Chagai Friedlander Dec 8 '19 at 23:38
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I use yeah or yep/yup when speaking casually. I tend to use yep/yup when it is being spoken by itself. I also would correspondingly use nope in the same way.

Did you do it?

Yeah, I did it

Yep.

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    +1. "Yep" has that self-sufficient feel, as if it had a period attached to it. "Yeah", on the other hand, feels like it has a comma attached, inviting me to expand on it. "Yeah, I did it", "yeah, that's right", "yeah, we really should do that" and so on. – RegDwigнt Aug 25 '10 at 19:39
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    Yup, I agree with you. – Zerotoinfinity Aug 31 '10 at 12:54
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Yes is not a formal word; you can use it in both formal and informal contexts.

Looking at the definitions given for yeah, yeh, yep, or yup, all those words are defined as exclamation & noun nonstandard spelling of yes, representing informal pronunciation.
Looking at the examples provided from the Werriam-Webster Online, it seems that yeah, and yep are used in two different cases. Yep is used when it's the only word in the answer; yeah is used in the other cases.

That's really what she said?
Yep.

That looks good.
Yeah, I think so too.

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    I agree definitely with the first part; yes can be used in informal situations without sounding formal, but I disagree on the second point; there is definitely a pragmatic difference among yeah, yup, and other variants. – Kosmonaut Aug 25 '10 at 18:36
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Yeah can also be used in a partial negation [yeah, but] meaning that you are affirming only a portion of the question.

Friend: Did you get movie tickets for me with the money I gave you?

You: Yeah, but they cost ten dollars more than you gave me for them. Would you be willing to pay for the popcorn?

Friend: Yep.

You: OK. See you there.

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3

In spoken (and informal written) English, I generally use yeah or yup.

I mostly use yes when additional emphasis is needed, possibly with additional words as confirmation, e.g. if someone said I hadn't completed a task, I might reply Yes, I did.

In formal written English, Yes should be used. You might see this, for example, on application forms which have Yes/No tick boxes or similar.

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Usually people write yes, unless it is informal writing, then yeah and yep can be used. In spoken English yes is always appropriate, but with friends and relations yeah and yep are frequently used. Sometimes the words can carry more meaning by their tone and repetition.

Mother: "Did you you do your homework yet?" Child: "yeah, yeah, yeah." (The homework not done, but the child is tired of being told about it.)

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When agreeing with someone I prefer "yeh" whereas with an exclamation such as "yeah, he scored the winning goal" the "yeah" is cognitively quicker to come off the mind than discerning first whether you want to spell it "yeh" or "yeah" knowing that the latter has more than one meaning.

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