Polygenic Score (PGS) ID: PGS012524

Predicted Trait
Reported Trait HDL cholesterol
Mapped Trait(s) high density lipoprotein cholesterol measurement (EFO_0004612)
Additional Trait Information Continuous lipid trait representing circulating high-density lipoprotein cholesterol (HDL-C) levels. Summary statistics used for polygenic score development were obtained from a multi-ethnic genome-wide association study conducted in the Million Veteran Program (PMID: 30275531).
Released in PGS Catalog: June 17, 2026
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Score Details

Score Construction
PGS Name HDL_LD
Development Method
Name LDpred
Parameters Polygenic score constructed using clumping and thresholding (LDpred) with genome-wide significant variants derived from MVP GWAS summary statistics
Variants
Original Genome Build GRCh38
Number of Variants 524,956
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000786
Citation (link to publication) Huang YJ et al. Nat Commun (2026)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 72.4%
African: 19.3%
Hispanic or Latin American: 8.3%
297,626 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 100%
  • European
  • African
  • Hispanic or Latin American
  • Additional Asian Ancestries
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST006611
Europe PMC: 30275531
 215,551 individuals European NR
GWAS Catalog: GCST006611
Europe PMC: 30275531
 57,332 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST006611
Europe PMC: 30275531
 24,743 individuals Hispanic or Latin American 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
PPM030596 PSS012196|
Multi-ancestry (including European)|
42,931 individuals
 PGP000786 |
Huang YJ et al. Nat Commun (2026)
 Reported Trait: High-density lipoprotein cholesterol levels β: 5.593 (0.138) — — sex, age, age^2, BMI, 11 genetic PCs Effect estimate corresponds to PRS per SD adjusted for genetic PCs.
PPM030598 PSS012196|
Multi-ancestry (including European)|
42,931 individuals
 PGP000786 |
Huang YJ et al. Nat Commun (2026)
 Reported Trait: High-density lipoprotein cholesterol levels β: 5.526 (0.137) — — sex, age, age^2, BMI, global ePRS Effect estimate corresponds to residual PRS (rPRS) adjusted for global expected PRS (gePRS).
PPM030597 PSS012196|
Multi-ancestry (including European)|
42,931 individuals
 PGP000786 |
Huang YJ et al. Nat Commun (2026)
 Reported Trait: High-density lipoprotein cholesterol levels β: 5.522 (0.137) — — sex, age, age^2, BMI, global ancestry proportions Effect estimate corresponds to PRS per SD adjusted for global ancestry proportions.

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
PSS012196 — — 22,909 individuals — European — OOA —
PSS012196 — — 10,323 individuals — African American or Afro-Caribbean — OOA —
PSS012196 — — 8,961 individuals — Hispanic or Latin American — OOA —
PSS012196 — — 738 individuals — Asian unspecified — OOA —