c.001A>C   11  p.His103    A
 c.000A>C   12  p.Thr102    E
 c.111A>C   12  p.Thr102    D

APC 5   112835056   ENST00000507379 13  c.001A>C    p.Val599Phe
APC 5   112819143   ENST00000257430 9   c.1111G  p.G371X
APC 5   1128395514  ENST00000257430 15  c.001A>C     p.Glu1309AspfsT
APC 5   112838773   ENST00000257430 15  c.000A>C    p.Gln1062Ter

APC 5   112835056   ENST00000507379 13  c.001A>C    p.Val59   c.001A>C  11  p.His103    A
APC 5   1128395514  ENST00000257430 15  c.001A>C    p.Glu1    c.001A>C  11  p.His103    A
APC 5   112838773   ENST00000257430 15  c.000A>C    p.Gln10   c.000A>C  12  p.Thr102    E


awk -F't' -v OFS="t" 'FNR==NR{a[$1]=$1FS$2FS$3FS$4; next} {if ($6 in a) print $0, a[$1]}' file1 file2

$ join -1 1 -2 6 -o "2.1 2.2 2.3 2.4 2.5 2.6 2.7 1.3 1.4" <(sort file1) <(sed 's/ +/ /g' file2 | sort -k6) | column -t
APC  5  112838773   ENST00000257430  15  c.000A>C  p.Gln1062Ter     p.Thr102  E
APC  5  1128395514  ENST00000257430  15  c.001A>C  p.Glu1309AspfsT  p.His103  A
APC  5  112835056   ENST00000507379  13  c.001A>C  p.Val599Phe      p.His103  A