Reference genome version between variant calling and annotation

Dear colleagues,

My project is focused on the annotation of human genetic variants (SNPs and short InDels) of WGS and WES.

I am using SNPEff version 5.0. In the snpeff config file I found

• GCA_000001405.28_GRCh38.p13
• Homo sapiens (hg38) (UCSC).

In contrast, the reference that was used for mapping and variant calling is GCA_000001405.15_GRCh38.

I would like to know if I used one of these two genomes in annotation, could that affect or bias my annotations?

Thanks in advance,
Adham,