Polygenic Score (PGS) ID: PGS005279

Predicted Trait
Reported Trait Body mass index (BMI)
Mapped Trait(s) body mass index (EFO_0004340)
Released in PGS Catalog: Aug. 6, 2025
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Terms and Licenses
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Score Details

Score Construction
PGS Name Q001_BMI_cutRSQ0.3_LD_rho0.03
Development Method
Name LDpred
Parameters ρ=0.03
Variants
Original Genome Build GRCh37
Number of Variants 5,000,812
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000751
Citation (link to publication) Sutoh Y et al. J Hum Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
East Asian: 100%
158,284 individuals (100%)
Score Development/Training
East Asian: 100%
9,811 individuals (100%)
PGS Evaluation
East Asian: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004904
Europe PMC: 28892062
 158,284 individuals East Asian 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
— 9,811 individuals,
34.8 % Male samples
 East Asian
(Japanese)		 IMM, ToMMo — Mean = 60.6 years
Sd = 11.2 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
PPM022764 PSS012075|
East Asian Ancestry|
11,947 individuals
 PGP000751 |
Sutoh Y et al. J Hum Genet (2024)
 Reported Trait: body mass index [BMI] — — R²: 0.069 age, age^2, sex, genetic PCs (1-10) The BMI was subjected to a natural logarithmic transformation and adjusted for covariates. Then, the residuals were processed using a rank-based normal transformation.
PPM022765 PSS012077|
East Asian Ancestry|
6,796 individuals
 PGP000751 |
Sutoh Y et al. J Hum Genet (2024)
 Reported Trait: body mass index [BMI] — — R²: 0.06 age, age^2, sex, genetic PCs (1-10) The BMI was subjected to a natural logarithmic transformation and adjusted for covariates. Then, the residuals were processed using a rank-based normal transformation.
PPM022766 PSS012076|
East Asian Ancestry|
50,195 individuals
 PGP000751 |
Sutoh Y et al. J Hum Genet (2024)
 Reported Trait: waist circumference [WC] — — R²: 0.039 age, age^2, sex, genetic PCs (1-10) The WC was adjusted for covariates. Then, the residuals were processed using a rank-based normal transformation.
PPM022768 PSS012077|
East Asian Ancestry|
6,796 individuals
 PGP000751 |
Sutoh Y et al. J Hum Genet (2024)
 Reported Trait: waist circumference [WC] — — R²: 0.04 age, age^2, sex, genetic PCs (1-10) The WC was adjusted for covariates. Then, the residuals were processed using a rank-based normal transformation.
PPM022763 PSS012076|
East Asian Ancestry|
50,195 individuals
 PGP000751 |
Sutoh Y et al. J Hum Genet (2024)
 Reported Trait: body mass index [BMI] — — R²: 0.063 age, age^2, sex, genetic PCs (1-10) The BMI was subjected to a natural logarithmic transformation and adjusted for covariates. Then, the residuals were processed using a rank-based normal transformation.
PPM022767 PSS012075|
East Asian Ancestry|
11,947 individuals
 PGP000751 |
Sutoh Y et al. J Hum Genet (2024)
 Reported Trait: waist circumference [WC] — — R²: 0.043 age, age^2, sex, genetic PCs (1-10) The WC was adjusted for covariates. Then, the residuals were processed using a rank-based normal transformation.

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
PSS012075 — — 11,947 individuals,
24.4 % Male samples
 Mean = 58.0 years
Sd = 12.9 years		 East Asian
(Japanese)		 — ToMMo —
PSS012076 — — 50,195 individuals,
39.1 % Male samples
 Mean = 60.4 years
Sd = 11.3 years		 East Asian
(Japanese)		 — IMM, ToMMo —
PSS012077 — — 6,796 individuals,
33.2 % Male samples
 Mean = 55.7 years
Sd = 13.5 years		 East Asian
(Japanese)		 — IMM —