Issues

• Verify version for gnomAD exomes & genomes used in VeP cache

  Ensembl/ensembl-vep#2075 · Filter by author damianosmel opened on Nov 6, 2026
  

• --custom reciprocal=1 is no longer a reciprocal overlap since 116 (PR #1944): no setting now requires both SVs to cover ≥ overlap_cutoff of each other

  Ensembl/ensembl-vep#2074 · Filter by author davmlaw opened on Nov 3, 2026
  2

  

• Terms of use for the SIFT and PolyPhen-2 predictions in the VEP cache

  Ensembl/ensembl-vep#2071 · Filter by author psklarkins opened on Oct 29, 2026
  6

  

• Breakend with INFO/CHR2 and INFO/END gets a false second breakend

  Ensembl/ensembl-vep#2070 · Filter by author awgymer opened on Oct 27, 2026
  1

  

• Plugins repeat transcript-independent lookup and allele matching per transcript allele: a per-variant cache helper in BaseVepPlugin cuts CPU 25% on coding input, output identical

  Ensembl/ensembl-vep#2069 · Filter by author davmlaw opened on Oct 26, 2026
  1

  

• Docs: suggest tabix -C -m 12 (4 kb CSI) as an alternative index for custom/plugin annotation files - several times faster lookups for a larger index, no code change

  Ensembl/ensembl-vep#2068 · Filter by author davmlaw opened on Oct 26, 2026
  

• Symbolic inversion receives start_retained_variant without a retention check; sequence-resolved equivalent does not (116.3)

  Ensembl/ensembl-vep#2065 · Filter by author paulstothard opened on Oct 15, 2026
  1

  

• Symbolic INV start_lost disappears when an endpoint enters an intron despite continued start-codon overlap (116.3)

  Ensembl/ensembl-vep#2064 · Filter by author paulstothard opened on Oct 15, 2026
  1

  

• Enhancement: distinguish partial-CDS inversions from intronic or whole-transcript inversions (116.3)

  Ensembl/ensembl-vep#2063 · Filter by author paulstothard opened on Oct 15, 2026
  1

  

• Lowercase insertion alleles with SVTYPE take a different parser path and can acquire spurious HIGH consequences (116.3)

  Ensembl/ensembl-vep#2062 · Filter by author paulstothard opened on Oct 15, 2026
  1

  

• VEP offline have issue processing chromosome not in cache

  Ensembl/ensembl-vep#2061 · Filter by author psun4782 opened on Oct 8, 2026
  3

  

• VEP installation problem

  Ensembl/ensembl-vep#2055 · Filter by author ascialla opened on Sep 24, 2026
  9

  

• VEP issue with HGVS description for an exonic 93 bp insertion

  Ensembl/ensembl-vep#2049 · Filter by author xm1zq2 opened on Sep 3, 2026
  1

  

• --check_frequency treats an allele frequency of exactly 0 as missing, dropping the rarest variants under --freq_filter include --freq_gt_lt lt

  Ensembl/ensembl-vep#2048 · Filter by author davmlaw opened on Sep 2, 2026
  1

  

• Add option to select only ensembl in merged database

  Ensembl/ensembl-vep#2046 · Filter by author antonylebechec opened on Aug 31, 2026
  2

  

• BAM_EDIT=FAILED for RefSeq NM_001372044.2 (SHANK3) leading to incorrect HGVSc coordinates

  Ensembl/ensembl-vep#2044 · Filter by author jkmatila opened on Aug 26, 2026
  

• Context deadline exceeded

  Ensembl/ensembl-vep#2036 · Filter by author robert-a-forsyth opened on Aug 10, 2026
  1

  

• --shift_3prime 1 produces non-standard c.*-N HGVSc for intronic insertions near stop codon

  Ensembl/ensembl-vep#2020 · Filter by author superbsky opened on Jun 22, 2026
  2

  

• Wrong coding change on a GRCh37 splicing site variant

  Ensembl/ensembl-vep#2006 · Filter by author milena-andreuzo opened on Apr 30, 2026
  

• HGVSg and HGVSc notation generated by the REST API response are incorrect for some variants

  bughgvs
  Ensembl/ensembl-vep#1984 · Filter by author Karthik-Tempus opened on Mar 15, 2026
  6

  

• HGNC_ID depends on buffering / input context (non-deterministic)

  bug
  Ensembl/ensembl-vep#1959 · Filter by author julius-muller opened on Dec 18, 2025
  3

  

• Obtain intron c. offset using REST API

  Ensembl/ensembl-vep#1953 · Filter by author rickymagner opened on Dec 4, 2025
  2

• Associate merge option and gencode_primary

  Ensembl/ensembl-vep#1952 · Filter by author jpofmars opened on Dec 4, 2025
  1

• inframe_insertion exclusively annotated as protein_altering_variant

  documentation
  Ensembl/ensembl-vep#1949 · Filter by author Redmar-van-den-Berg opened on Nov 26, 2025
  5

  

• feature request: Optimized cache format

  enhancement
  Ensembl/ensembl-vep#1947 · Filter by author feiloo opened on Nov 24, 2025
  3