Allele Frequencies in World Populations

HLA Database » Rare Alleles

This module describes all classical HLA alleles registered on the IMGT/HLA Database as of Release 3.20.0 and the number of times that each allele has been reported to different databases such as the Allele Frequency Net Database (AFND), the National Marrow Donor Program (NMDP) in the US as of Release 3.9.0 and other individual laboratories.

The aim of this page is that a user can identify HLA rare alleles by filtering the total times an HLA allele has been reported to these Databases.
E.g. Cells < 3, Groups < 3, Pops < 2, NMDP < 2, Labs < 2.

Contribute to this project

This project was included in the 16th International HLA and Immunogenetics Worskhop (IHWS) in Liverpool (28-30 May 2012) and has been published in International Journal of Immunogenetics 2013 40:60-65 [See abstract]. Results from the 15th IHWS were published in Tissue Antigens 2009 74:480-485 [See abstract].

If an allele that we consider to be rare has been typed in your laboratory, please report it by clicking on the "" image beside the allele. Basic information will be required to complete your submissions. Your contribution is vital to confirm the number of rare alleles!. Click here to see the list of current contributors.

New tool: Rare Allele Detector

To facilitate the analysis of large datasets (i.e. 1000 individuals typed) the Rare Allele Detector tool has been incorporated to the AFND website. This tool simplifies the detection of alleles which are considered to be very rare, rare or frequent. Click here to try this tool.

How to browse

Rare alleles can be filtered according to how many times it is since they were first sequenced. Please select your criteria by using different options and click "Search".

Search Allele:  To consult the equivalent code for the previous nomenclature click here.
Locus:      IMGT/HLA Cells:      Groups:      Pops AFND:      NMDP Total:      Other Labs: 
Combining sources : (IMGT/HLA + Website + NMDP + Other Labs)         Year of first sequence in IMGT/HLA :         ASHI : 

Typing Method : 
Group identical alleles over exons 2 + 3 ¹
Displaying 1 to 30 (from 12,686) records Pages: 1 2 3 4 5 6 7 8 9 10 of 423
IMGT/HLA Allele Frequencies Website IMGT/HLA
(See details)
(See details)
Other Labs
(See details)
Allele Pops with allele in website See lower resolution See sequences identical over exons 2 + 3 ¹ Allele initially sequenced in population Year Sequence confirmed Cells Groups Length Total AFA API CAU HIS NAM OTH Total BLA CAU MES HIS OTH
1A*01:01:01:016A*01:01, A*01:01:01A*01:01:01:02N, A*01:01:38L, A*01:01:51, A*01:04N, A*01:103, A*01:107, A*01:109, A*01:132, A*01:141, A*01:142, A*01:22N, A*01:32, A*01:37, A*01:45, A*01:56N, A*01:81, A*01:87NCaucasoid - England, Europe; Caucasoid - Netherlands, Europe; Caucasoid - South Africa, Southern Africa; Oriental - China, Asia; Oriental - Chinese, China, Asia1989Confirmed78Full-NA>4C/WD US
2A*01:01:01:02N  0A*01:01, A*01:01:01A*01:01:01:01, A*01:01:38L, A*01:01:51, A*01:04N, A*01:103, A*01:107, A*01:109, A*01:132, A*01:141, A*01:142, A*01:22N, A*01:32, A*01:37, A*01:45, A*01:56N, A*01:81, A*01:87NCaucasoid - Spain, Europe2005Unconfirmed11Full-112
3A*01:01:02  1A*01:01Mixed - American Indian/Caucasoid2000Unconfirmed11Partial--2
5A*01:01:04  0A*01:01Unknown2006Unconfirmed11Partial--1
6A*01:01:05  0A*01:01Caucasoid - Germany, Europe2007Unconfirmed11Partial--1
8A*01:01:07  0A*01:01Unknown2009Unconfirmed11Partial-112
9A*01:01:08  0A*01:01Unknown2009Unconfirmed11Partial--1
13A*01:01:12  0A*01:01Unknown2009Confirmed21Partial-113
15A*01:01:14  0A*01:01Unknown2010Unconfirmed11Partial--1
16A*01:01:15  0A*01:01Oriental - Korea, Asia2010Confirmed22Partial--2
18A*01:01:17  0A*01:01Unknown2010Confirmed41Partial--4
19A*01:01:18  0A*01:01Unknown2010Confirmed21Partial--2
20A*01:01:19  0A*01:01Unknown2010Confirmed21Partial--2
21A*01:01:20  0A*01:01Caucasoid - Unknown, Western Europe2010Unconfirmed11Partial--1
22A*01:01:21  0A*01:01Unknown2010Unconfirmed11Partial--1
23A*01:01:22  0A*01:01Unknown2010Confirmed42Partial--4
24A*01:01:23  0A*01:01Unknown2010Unconfirmed11Partial--1
25A*01:01:24  0A*01:01Unknown2010Unconfirmed11Partial--1
26A*01:01:25  0A*01:01Unknown2010Unconfirmed11Partial--1
27A*01:01:26  0A*01:01Unknown2010Confirmed22Partial--2
28A*01:01:27  0A*01:01Unknown2010Unconfirmed11Partial--1
29A*01:01:28  0A*01:01Unknown2010Unconfirmed11Partial--1
30A*01:01:29  0A*01:01Unknown2010Confirmed21Partial--2

Displaying 1 to 30 (from 12,686) records   Pages: 1 2 3 4 5 6 7 8 9 10 of 423  

Report Information


  • Year. Year of the first sequence submitted.
  • Sequence confirmed. If an allele has been sequenced by more than a single laboratory or from multiple sources (E.g. Cells, DNA).
  • Cells. Number of cells/sources which have been sequenced for that allele.
  • Groups. Number of submitters who have sequenced the allele.
  • Length. Coding Sequence (CDS).

National Marrow Donor Program (NMDP)

  • AFA. African American
  • API. Asian or Pacific Islander
  • CAU. Caucasian
  • HIS. Hispanic Race or Ethnicity with CAU or no race
  • NAM. Native American
  • OTH. Multiple, Unknown or Decline
  • Notes:
      Only A, B, C and DRB1 loci were reported by NMDP in this release.
      (-) Allele not reported at this level of resolution.

Other Laboratories

  • BLA. Black
  • CAU. Caucasian
  • MES. Mestizo
  • HIS. Hispanic
  • OTH. Other
  • Notes:
      NA. The allele was not asked to individual laboratories as the allele was considered frequent.
      (-) Allele has not been confirmed by any laboratory yet.

American Society for Histocompatibility and Immunogenetics (ASHI)

  • C/WD = Common and Well Documented allele.
  • US = C/WD alleles found frequently in subjects living in the United States.

    Cano P, Klitz W, Mack SJ, Maiers M, Marsh SG, Noreen H, Reed EF, Senitzer D, Setterholm M, Smith A, Fernandez-Viña M. Common and well-documented HLA Alleles: report of the Ad-Hoc committee of the american society for histocompatibility and immunogenetics. Hum Immunol. (2007); 68(5):392-417.
  • ^ = A lower resolution was reported by Cano et al.

  • Notes:
      The list of C/WD alleles reported by Cano et al 2007 was updated on November 2007 by Marcelo Fernandez-Viña including DPA1 locus.


  • Total = Allele Frequency Website + IMGT/HLA Confirmations (Cells including initial confirmation) + NMDP + Other Labs

Colour Code

              ¹ Sequences identical:
  • over exons 2 + 3 for HLA-A, -B and -C loci
  • over exons 2 for HLA-DPB1, -DQA1, -DQB1 and -DRBn loci
  • over region nt 101 to 356 for HLA-DRB1 locus

Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations.
Gonzalez-Galarza FF, Takeshita LY, Santos EJ, Kempson F, Maia MH, Silva AL, Silva AL, Ghattaoraya GS, Alfirevic A, Jones AR and Middleton D Nucleic Acid Research 2015, 39, 28, D784-8.
Liverpool, U.K.

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