Species subgroup
Subgroup type
Sequence NameIGHV4-39*09
IUIS NameIGHV4-39*09
Alternative namesIGHV4-39*i02
Affirmation Level1
Full Sequence
Coding Sequence
Inference TypeRearranged Only
Paralog RepFalse

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

VDJbase Allele NameSubjectsSequence Match
IGHV4-39*07_c288a 4

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:


CDR delineation

CDR1 Start76
CDR1 End105
CDR2 Start157
CDR2 End177
CDR3 Start292


3' ExtensionA
3' start
3' end

Additional Information

Sequence IDA00071
CuratorWilliam Lees
Curator addressBirkbeck College, University of London, Malet Street, London
Release Date2023-07-10
Release Notes

Bulk upload of sequences for the AIRR-C Human IG germline sets

Sequence TypeV
Gene Subgroup4
Gene Designation39
Allele Designation09


Individuals acknowledged as contributing to this sequence:

No Items


Notes are added by IARC reviewers.

IARC meeting 63, Nov 24th, 2020:
The meeting considered the inference of the variant IGHV4-39*07_c288a in the VDJbase datasets of sample P1_I29_S1. (It was present in two other VDJbase samples). The sequence was seen in 4.61% of all unmutated rearrangements, with 1201 sequences including 1068 perfect matches to the inferred allele. There was abundant variation in the CDR3 regions of the aligned sequences. IGHV4-39*01 was also present in the genotype, at a similar frequency (4.35% of all unmutated sequences, 1135 sequences, 1009 unmutated sequences). Plots of the final 3’ nucleotides were unavailable. Haplotyping data strongly supported the inference. The sequence was tentatively affirmed as a Level 1 sequence, and the final 3’ nucleotides will be considered at a later date, when terminal nucleotide plots become available, at which time the affirmed sequence will be noted in the IARC minutes.

IARC-meeting 84, Oct 25th, 2021:
IGHV4-39*07_C288A was inferred in subject S29 (VDJ-base: P1_I29_S1). This inference has previously been pre-assessed at IARC meeting 63 ( The genotype also carried IGHV4-39*01. The inference was supported by many sequences (1304) and unmutated sequences (1107) a balanced allelic frequency (52%), a high overall frequency in the unmutated population (5.7%) and many unique CDR3s (1086) in the unmutated sequence set. Haplotyping based on allelic diversity in IGHJ6 was possible and the alleles distributed well between haplotypes (IGHV4-39*07_C288A: 99:1; IGHV4-39*01: 0:100). IARC infers the sequence at level 1 up to and including base 319 in agreement with past practice. It is acknowledged that the allele most likely carry one additional base, typically A at base position 320. The allele is given the name IGHV4-39*i02.

>IGHV4-39*i02 (IGHV4-39*07_C288A)

Additional information for this sequence was imported into OGRDB via bulk update with the following notes:
Sequence annotation is based on Genbank sample OU596103
VDJbase example haplotype: P1_I29 (*07_c288a)
VDJbase example haplotype: P1_I29 (*07_c288a)
Mapped by P1_I29 haplotype


No Items


History logs the times and reasons for the publication of each version of this sequence.

Mats Ohlin
2021-11-01 22:50:46
Version 1 published

Submission published by IARC on November 1st, 2021

Mats Ohlin
2021-11-17 15:25:43
IMGT Name updated to IGHV4-39*09

IMGT Name updated.

William Lees
2023-07-10 11:24:41
Version 2 published

Bulk upload of sequences for the AIRR-C Human IG germline sets

Changes from previous version

CuratorMats OhlinWilliam Lees
Curator addressDept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, SwedenBirkbeck College, University of London, Malet Street, London
Sequence NameIGHV4-39*i02IGHV4-39*09
Alternative namesIGHV4-39*i02
Subgroup typenone
Allele Designationi0209
Full Sequence
Codon Frame1
Paralog RepFalse
3' ExtensionA
5' Extension


All published versions of this sequence.

Sequence NameIMGT NameAlternative namesInference TypeAffirmation LevelSpecies subgroupSubgroup typeGene startGene endUTR 5' StartUTR 5' EndL-PART1 StartL-PART1 EndL-PART2 StartL-PART2 EndCDR1 StartCDR1 EndCDR2 StartCDR2 EndCDR3 Startv_rs_startv_rs_endd_rs_3_prime_startd_rs_3_prime_endd_rs_5_prime_startd_rs_5_prime_endj_rs_startj_rs_endCodon FrameVersionDate
IGHV4-39*i02IGHV4-39*09Rearranged Only1none129876105157177292112021-11-01
IGHV4-39*09IGHV4-39*09IGHV4-39*i02Rearranged Only112987610515717729222023-07-10