you intput data is really nice: space, comma, semicolon... try this:
awk -F'[;, ]' '{n=0;s=0;for(i=1;i<=NF;i++)
if($i~/=[0-9]+/){split($i,t,"=");n++;s+=t[2]; }
print $0"AF="s/n";"
}' file
with your data:
kent$ echo "1 11 11 T A 0 0 A=1;B=2,C=3;D=4;"|awk -F'[;, ]' '{n=0;s=0;for(i=1;i<=NF;i++)
if($i~/=[0-9]+/){split($i,t,"=");n++;s+=t[2]; }
print $0"AF="s/n";"
}'
1 11 11 T A 0 0 A=1;B=2,C=3;D=4;AF=2.5;