Missing exon/intron in annotation with --shift_3prime 1

[karlestira]

Describe the issue

When using --shift_3prime 1, VEP do not give exon/intron annotation.

Additional information

Input vcf:
chr7 55248980 . C CTCCAGGAAGCCT

Vep result without --shift_3prime 1 (show one of the transcript):
chr7 55248980 . C CTCCAGGAAGCCT . . CSQ=TCCAGGAAGCCT|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|EGFR|ENSG00000146648|Transcript|ENST00000275493|protein_coding||19/27|ENST00000275493.2:c.2284-5_2290dup|||||||||1||HGNC|3236||Ensembl||12

Vep result with --shift_3prime 1 (show one of the transcript):
chr7 55248980 . C CTCCAGGAAGCCT . . CSQ=TCCAGGAAGCCT|inframe_insertion|MODERATE|EGFR|ENSG00000146648|Transcript|ENST00000275493|protein_coding|||ENST00000275493.2:c.2284-5_2290dup|ENSP00000275493.2:p.Ala763_Tyr764insPheGlnGluAla|2467-2468|2290-2291|764|Y/FQEAY|tac/tTCCAGGAAGCCTac|||1||HGNC|3236||Ensembl||12

When enable 3prime shift, the intron number lost, but no exon number shown, this affect all transcript(include refseq and ENST).

System

• VEP version: v112.0
• VEP Cache version: v112.0 GRCh37 homo_sapiens_merged
• Perl version: 5.26.2
• OS: Debian GNU/Linux 10 (buster)
• tabix installed ? : tabix 1.14

Full VEP command line

vep --input_file test.vcf --output_file test.vep.shift3.vcf --dir_cache /vep_db --format vcf --vcf --symbol --biotype --hgvs -fasta /Genome/hg19/ucsc.hg19.fa --offline --cache --merged --use_given_ref --shift_3prime 1

Full error message

No error message

Data files (if applicable)

[nakib103]

Hi @karlestira,

Thanks for your query!

When you use --shift_3prime 1 it calculates the exon and intron number after the shift. With the 12bp shift here the variant goes to exon-intron boundary. Unfortunately we have some known complications regarding annotating variants that overlaps exon-intron boundary (see #1155, #1482) and here, in this case, it does not report exon or intron number.

Best regards,
Nakib