The most common and most likely answer to this crossword clue is the 6 letter word ASYLUM
I've seen this crossword clue in The Times
A
S
Y
L
U
M
More clues leading to the result ASYLUM
- Refuge from years in a favela
- Fantastic sum lay in a safe place
- Shelter a poor area bringing in yen
- Shelter unknown character in a deprived area
- Place of safety unknown in a squalid urban area
- A year in mean accommodation provides sanctuary
- Shelter Yankee in a poor part of Harlem?
- Shelter’s variable in a humble dwelling
- Shelter unknown character found in a poor part of town
- Shelter Yankee in a squalid neighbourhood
Buddy explains!

The straight part
We know that "Shelter" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case shelter = asylum.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 ASYLUM mean?
ASYLUM noun- A place of safety.
- The protection, physical and legal, afforded by such a place.
- A place of protection or restraint for one or more classes of the disadvantaged, especially the mentally ill.