Polygenic Score (PGS) ID: PGS005243

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Oct. 6, 2025
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Terms and Licenses
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Score Details

Score Construction
PGS Name T2D_PRS_PRS_CSx_META_F_AFR
Development Method
Name PRS-CSx
Parameters This AFR population specific PRS score was developed using the META=F function in PRS-CSx. The T2D GWAS summary statistics used to develop the PRS were from the AFR population from Vujkovic et al., 2020 (doi:10.1038/s41588-020-0637-y) ,which included 24,646 AFR T2D cases and 31,446 AFR controls. Linkage disequilibrium (LD) reference panels were based on the 1000 Genomes Project (1KG) Phase 3 participants from AFR population samples.
Variants
Original Genome Build GRCh37
Number of Variants 1,183,017
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000742
Citation (link to publication) Guo B G et al. Nat Commun (2025)
Ancestry Distribution
Source of Variant
Associations (GWAS)
African: 100%
56,092 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010556
Europe PMC: 32541925
 56,092 individuals African American or Afro-Caribbean NR

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM022724 PSS012058|
African Ancestry|
13,161 individuals
 PGP000742 |
Guo B G et al. Nat Commun (2025)
 Reported Trait: Type 2 diabetes OR: 1.23 [1.19, 1.26] AUROC: 0.664 [0.657, 0.671] — age, sex, BMI, sub-study, and first 10 PCs —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS012058 — —
[
  • 5,429 cases
  • , 7,732 controls
]
,
43.8 % Male samples
 Mean = 58.9 years
Sd = 9.99 years		 African unspecified
(African American)		 — PAGE —