Kanji reading "exceptions" in native japanese words

I have a question, noticed that 煙管 a japanese smoking pipe is キセル I’m guessing this reading is an exception? but it also shows that it can be read as えんかん how do you know which reading to use and when?

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Sometimes in Japanese they end up choosing kanji for a word that represent the meaning more than the reading. For example you can sometimes see these kanji 煙草 instead of the kana word. At level 26 you might be able to guess what it means.

This happens sometimes, though not very often, as far as I have seen. An example of the opposite is kanji chosen for their readings, that have nothing to do with the actual thing being expressed. 寿司 for example.

These are 当て字, and you just hsve to learn them as they cross your path. Or at least make a note of it in the back of your mind, if it is not a super common one.

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Also in this specific case we are talking about a loanword (like 珈琲=コーヒー),where a non-Japanese concept is assigned kanji, maybe in order to clarify the meaning? And I am guessing that after that キセル became (or already was) such an obscure word, that people just started reading it by the on’yomi

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