I understood that this sentence means, it's not worth the trouble, but, Why is there 'en' between ne and vaut? What does it signify? Is it a pronoun?
In which other connotations can "en" be used?
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This "en" means "de le faire" (The "doing" in "It's not worth doing"). The sentence without "en" would be :
ça ne vaut pas la peine de le faire
"En" can be used when when you have a verb using the preposition "de", for example :
J'ai mangé de la tarte.
If the pie was already mentioned before, you could just use "en" instead :
Mr X : As-tu mangé de la tarte ?
Mr Y : Oui, j'en ai mangé.