Cryptic crossword clue
Ran through church in country 6

The most common and most likely answer to this crossword clue is the 6 letter word LANCED

I've seen this crossword clue in The Guardian
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The straight part
We know that "Ran through" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case ran through = lanced.
The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.
This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.

What does LANCED mean?

LANCED verb
  1. To pierce with a lance, or with any similar weapon.
  2. To open with a lancet; to pierce
  3. To throw in the manner of a lance; to lanch.

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