I have a same variant obtained once on GRCH37 and once on GRCH38 I want to annotate it with VEP to obtain the HGVS annotation. So I use VEP (v100) to annotate both variants.
On GrcH37, the variant is annotated with NM_001160184.1, while for GRCH38, this variant is annotated with NM_001160184.2.
It seems that the problem is due to the fact that VEP don't use the same RefSeq database (see : https://m.ensembl.org/info/docs/tools/vep/script/vep_cache.html)
2019-06-28 (GCF_000001405.39_GRCh38.p13_genomic.gff) for GRCh38 data 2019-11-01 (GCF_000001405.25_GRCh37.p13_genomic.gff) for GRCh37 data
Why VEP does not use use the same GFF file ? how to obtain the annotation with the same transcript on both genome versions ? (NM_001160184.1 for grch 37 and 38)