SnpSift in multiallelic variants

[rogeriobioinfo]

Dear,
I'm using SnpEff and SnpSift to annotate a vcf file containing biallelic and multiallelic variants. For multiallelic, variants i.e. C/A,T, SnpEff annotates each possible combination (C/A and C/T). On the other hand, SnpSift does only one annotation for this multiallelic variant, which means C/A,T . The SnpSift is considering only the C/A frequency when annotating C/A,T. Yet, there are only allele frequencies for C/A and C/T, but not for C/A,T in the database.
Rogério