use strict;
use warnings;

my %data;
while (<DATA>) {
    my @cols = split;
    my $col3 = pop @cols;
    my $key = "@cols";
    push @{ $data{$key} }, $col3;
}

for (keys %data) {
    print "$_ ", join(',', @{ $data{$_} }), "\n";
}

__DATA__
chr1 12345 34567 gene1 
chr1 12345 34567 gene2