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Human Genome Issue HG-79

Summary:
Chr.9 ABO haplotype issue
Description:
In this region, the ABO gene in the reference assembly reflects a haplotype of "Type O" not found in the human population.
Status:
Resolved (GRC Resolved by Experimental Method)
Type:
Variation
Last updated:
2014-10-10
Affects version:
NCBI36
Fix version:
GRCh37.p1
Resolution:
Component AL772161.10 has replaced component AL158826.23 in the reference assembly. The switch points between AL732364 and AL772161 have been curated to ensure that only one haplotype is represented. The ABO gene contained solely within AL772161 is a functional A1.02 allele. The updated version is available as a patch for GRCh37: GL339450.1 Despite being released as a GRCh37 FIX patch, this issue was not present in the GRCh38 primary assembly. This issue has now been addressed by the GRCh38.p1 FIX patch associated with ticket HG-2030

Patches and alternate loci

Scaffold type:
FIX patch to GRCh37
Comment:
This sequence will be incorporated into the reference assembly in the next major assembly release. At that time, the accession number for this patch will be made secondary to the reference chromosome accession. The ABO locus on GRCh37 NC_000009.11 is derived from two different haplotypes, resulting in a Type O allele not found in the human population.This patch provides a valid single haplotypic representation of the ABO locus representing the A2 allele.
Revision history of patches and alts for HG-79
Assembly Scaffold type Contig name GenBank accession RefSeq accession Region
GRCh37.p2 FIX HG79_PATCH GL339450.1 NW_003315925.1 ABO
GRCh37.p1 FIX HG79_PATCH GL339450.1 ABO

Locations and genomic context

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  • (View region: Ensembl | NCBI | UCSC)
  • (View region: Ensembl | NCBI | UCSC)