Incorrect HGVS.p annotation for variant when use transcript annotations defined in GFF file

[mt202202]

Describe the issue

when using transcript annotations defined in GFF file, VEP performed incorrect HGVS.p annotation for the variant chr10:87754701-CAT-C，NM_032810.4:c.1070_1071del (rs751499706)

when using transcript annotations defined in GFF file， VEP annotated the variant as NP_116199.2:p.His357ArgfsTer41, the correct annotation should be NP_116199.2:p.His357ArgfsTer15. When using Ensembl Genomes caches or using the web interface, the variant was annotated as NP_116199.2:p.His357ArgfsTer15(correct annotation result)

My project would like to be able to specify gff files for analysis

System

• VEP version: [108.2]
• VEP Cache version: [102]
• Perl version: [5.24]
• tabix installed :YES

Full VEP command line

vep -i tmp.vcf -o merge.VEP.txt --fasta hg38_merge.fa.gz --assembly GRCh38 --vcf --force --no_stats --hgvs --hgvsg --shift_3prime 1 --shift_length --total_length --no_escape --biotype --symbol --numbers --custom hg38//GCF_000001405.40_GRCh38.p14_110.20220713_genomic.ann.gff.gz,RefSeqGFF,gff --fields SOURCE,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,HGVSg,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,DISTANCE,STRAND,HGVS_OFFSET,SHIFT_LENGTH --fork 5

Full error message

Including the warnings, if available

[likhitha-surapaneni]

Hi @mt202202 , thank you for reporting this. We are currently investigating this further and will let you know once we have an update.

Kind regards, Likhitha