Details


Species	Human
Species subgroup
Subgroup type	none
Sequence Name	IGHV4-39*i03
IUIS Name
Alternative names	IGHV4-39*01 G315A
Affirmation Level	1
Full Sequence
Coding Sequence
Functionality	F
Inference Type	Rearranged
Mapped
Paralogs
Paralog Rep

Observations in VDJbase

Inferred sequences in VDJbase that match this sequence:

VDJbase Allele Name	Subjects	Sequence Match
IGHV4-39*01_g315a	3

Un-rearranged Observations

Un-rearranged sequence observations that support this sequence:

No Items

CDR delineation


CDR1 Start	76
CDR1 End	105
CDR2 Start	157
CDR2 End	177
CDR3 Start	292

Non-Core Regions


UTR 5' Start
UTR 5' End
L-PART1 Start
L-PART1 End
L_PART1
L-PART2 Start
L-PART2 End
L_PART2
v_rs_start
v_rs_end
V_HEPTAMER
V_NONAMER

Extension


3' Extension
3' start
3' end
5' start
5' end

Additional Information


Sequence ID	A02561
Curator	Mats Ohlin
Curator address	Dept. of Immunotechnology, Lund University, Medicon Village building 406, S-22381 Lund, Sweden
Version	2
Release Date	2023-06-02
Release Notes	A typographical error in the Notes section was corrected: “The genotype carried one other allele of IGHV4-39 (IGHV4-3101, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-3901).” was corrected to “The genotype carried one other allele of IGHV4-39 (IGHV4-3901, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-3901).”.
Locus	IGH
Sequence Type	V
Gene Subgroup	4
Gene Designation	39
Allele Designation	i03

Acknowledgements

Individuals acknowledged as contributing to this sequence:

No Items

Notes

Notes are added by IARC reviewers.


This inferred allele was assessed at IARC meeting 100 on June 8th, 2022. IGHV4-3901_G315A was inferred in subject S57 (VDJ-base: P1_I60_S1). The genotype carried one other allele of IGHV4-39 (IGHV4-3901, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-3901). The inference was supported by a large number of sequences (1424) and unmutated sequences (1151), a high overall frequency in the unmutated population (2.47%) and a large set of unique diverse CDR3s (1048) in the unmutated sequence set. It represented 48% of sequences associated with the gene. Haplotyping based on allelic diversity in IGHJ6 was not possible. IARC affirms the sequence at level 1 up to and including base 319 in agreement with past practice. It is acknowledged that the allele most likely carries one additional base, typically A at base position 320. A trailing “.” indicates IARC’s opinion that the sequence is likely to contain one additional 3’-nucleotides for which there is insufficient evidence to make an affirmation. The allele is given the name IGHV4-39i03.

This inferred allele was assessed at IARC meeting 100 on June 8th, 2022. IGHV4-39*01_G315A was inferred in subject S57 (VDJ-base: P1_I60_S1). The genotype carried one other allele of IGHV4-39 (IGHV4-39*01, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-39*01). The inference was supported by a large number of sequences (1424) and unmutated sequences (1151), a high overall frequency in the unmutated population (2.47%) and a large set of unique diverse CDR3s (1048) in the unmutated sequence set. It represented 48% of sequences associated with the gene. Haplotyping based on allelic diversity in IGHJ6 was not possible. IARC affirms the sequence at level 1 up to and including base 319 in agreement with past practice. It is acknowledged that the allele most likely carries one additional base, typically A at base position 320. A trailing “.” indicates IARC’s opinion that the sequence is likely to contain one additional 3’-nucleotides for which there is insufficient evidence to make an affirmation. The allele is given the name IGHV4-39*i03.

Attachments

No Items

History

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


Mats Ohlin 2022-07-25 10:54:25	Version 1 published The allele was published by IARC on July 25th, 2022.


Mats Ohlin 2023-06-02 14:44:22	Version 2 published A typographical error in the Notes section was corrected: “The genotype carried one other allele of IGHV4-39 (IGHV4-3101, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-3901).” was corrected to “The genotype carried one other allele of IGHV4-39 (IGHV4-3901, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-3901).”.

Mats Ohlin
2023-06-02 14:44:22

Version 2 published

A typographical error in the Notes section was corrected: “The genotype carried one other allele of IGHV4-39 (IGHV4-31*01, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-39*01).” was corrected to “The genotype carried one other allele of IGHV4-39 (IGHV4-39*01, and a variant allele with a low number of associated reads that likely represents 3’-trimmed reads of IGHV4-39*01).”.

Changes from previous version

	v1	v2
Notes		changed

Versions

All published versions of this sequence.

Sequence Name	Alternative names	Inference Type	Affirmation Level	Subgroup type	Gene start	Gene end	CDR1 Start	CDR1 End	CDR2 Start	CDR2 End	CDR3 Start	Codon Frame	Version	Date
IGHV4-39*i03	IGHV4-39*01 G315A	Rearranged	1	none	1	298	76	105	157	177	292	1	1	2022-07-25
IGHV4-39*i03	IGHV4-39*01 G315A	Rearranged	1	none	1	298	76	105	157	177	292	1	2	2023-06-02
IGHV4-39*i03		Rearranged Only	1		1	298	76	105	157	177	292		3	2023-07-10