Polygenic Score (PGS) ID: PGS003841

Predicted Trait
Reported Trait Height
Mapped Trait(s) body height (EFO_0004339)
Released in PGS Catalog: Sept. 1, 2023
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Score Details

Score Construction
PGS Name height_AFR_CTSLEB
Development Method
Name CTSLEB
Parameters w_b= (50kb, 100kb), , clumping r2=(0.01, 0.05, 0.1, 0.2, 0.5, 0.8) , clumping window size = w_b/r2, p-value threshold = c(5E-08,5E-07,...,0.5,1), super leaner method was set to be glmnet and ridge to obtain linear weight
Variants
Original Genome Build GRCh37
Number of Variants 741,637
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000489
Citation (link to publication) Zhang H et al. Nat Genet (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • Hispanic or Latin American
  • African
85,295 individuals (100%)
Score Development/Training
African: 100%
4,515 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 85,295 individuals,
42.0 % Male samples
 European, Hispanic or Latin American, African American or Afro-Caribbean NR
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 4,515 individuals,
42.0 % Male samples
 African American or Afro-Caribbean
(African American)		 UKB — Mean = 51.82 years
Sd = 8.06 years		 — — —

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
PPM018648 PSS011041|
African Ancestry|
4,527 individuals
 PGP000489 |
Zhang H et al. Nat Genet (2023)
 Reported Trait: Height — — R²: 0.03775 — —

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
PSS011041 — — 4,527 individuals,
42.0 % Male samples
 Mean = 51.82 years
Sd = 8.06 years		 African American or Afro-Caribbean
(African American)		 — UKB —