A simple solution: 
use strict;
my %chr_hash;
while(<DATA>)
{
    chomp;
    my ($chr, $start, $end, $gene) = split(/\t/, $_);
    my $chr_key = $chr."_".$start."_".$end;
    
    #print "$chr_key\n";
    push( @{ $chr_hash{$chr_key} }, $gene ); 
    
    
}

foreach my $key (keys %chr_hash)
{
    my ($c, $s, $e) = split(/\_/, $key ); 
    print "$c\t$s\t$e\t";
    for my $g ( @ {$chr_hash{$key} } )
    {
        print "$g,";
    }
    
    print "\n";
}


__DATA__
chr1    12345    34567    gene1 
chr1    12345    34567    gene2

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In reply to Re: Duplicate removal by umasuresh
in thread Duplicate removal by perl_paduan

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