If you can tolerate the change of square brackets to curly braces, it's easy:

#!/usr/bin/perl
use warnings;
use strict;

<DATA>; # Skip the header line


my %table;
while (<DATA>) {
    my ($chrom, $pos, $id, $ref, $alt, $qual) = split;
    $table{$chrom}{$pos} = {
                            REF  => $ref,
                            ALT  => $alt,
                            QUAL => $qual,
                           };
}

print $table{chr1}{1092482}{REF}, "\n";   # Prints T, yay!

__DATA__
#CHROM    POS    ID    REF    ALT    QUAL
chr1    1092344    .    G    T    79.54
chr1    1092367    .    C    T    148.50
chr1    1092400    .    G    C    90.54
chr1    1092424    .    A    G    93.14
chr1    1092461    .    G    A    105.30
chr1    1092470    .    T    G    103.06
chr1    1092482    .    T    C    104.33
chr1    1093235    .    G    A    16.08
chr1    1093245    .    C    T    244.75
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