This does the job:

my %data;

while (<DATA>)
{
    chomp;
    
    my ($firstnum, $secondnum, $thingy, @bits) = split /\s/;    
    my $key = sprintf("%s\x00%s\x00%s", $firstnum, $secondnum, $thingy
+);

    for my $i (0 .. $#bits)
    {
        $data{$key}[$i] = [] unless exists $data{$key}[$i];
        push @{ $data{$key}[$i] }, $bits[$i];
    }
}

foreach my $key (sort keys %data)
{
    print join q[ ], split "\x00", $key;
    print q[ ];
    print join q[ ], map { join '/', @$_ } @{ $data{$key} };    
    print "\n";
}

__DATA__
1 51 Brahui A C A A T 
1 51 Brahui A C A G T 
3 51 Brahui A C A G C 
3 51 Brahui A C G A T 
5 51 Brahui A C G A T 
5 51 Brahui A C G G C 
7 51 Brahui A C G A T 
7 51 Brahui A C G G T 
9 51 Brahui A C G G T 
9 51 Brahui A C G G T
[download]

But don't just copy that as-is. Try to understand how it works. What you want to look at is:

• "I/O Operators" in perlop.
• split, join and map - see perlfunc.
• perllol to teach you about nested data structures.