You could sort the elements, then store the stringified (comma-separated) sorted elements as hash keys, then print out just the hash keys:

use strict;
use warnings;

my %uniqs;
while (<DATA>) {
    chomp;
    my @list = split /,/;
    my @sorted = sort {$a <=> $b} @list;
    $uniqs{ join ',', @sorted }++;
}
print "$_\n" for keys %uniqs;

__DATA__
1,2,4
1,2,3
4,2,1
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prints:

1,2,4
1,2,3
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