Polygenic Score (PGS) ID: PGS002732

Predicted Trait
Reported Trait Chronic elevation of alanine aminotransferase
Mapped Trait(s) serum alanine aminotransferase measurement (EFO_0004735)
Released in PGS Catalog: July 21, 2022
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Score Details

Score Construction
PGS Name GRS_77
Development Method
Name Genome-wide significant variants
Parameters r2 > 0.05, p<5E-08
Variants
Original Genome Build NR
Number of Variants 77
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000341
Citation (link to publication) Vujkovic M et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 75.1%
African: 17.1%
Hispanic or Latin American: 6.9%
Additional Asian Ancestries: 0.9%
218,595 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 66.7%
  • European
  • Hispanic or Latin American
  • East Asian
  • South Asian
  • African
European: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
—
[
  • 95,472 cases
  • , 68,725 controls
]
 European MVP
—
[
  • 23,977 cases
  • , 13,387 controls
]
 African American or Afro-Caribbean MVP
—
[
  • 7,650 cases
  • , 7,468 controls
]
 Hispanic or Latin American MVP
—
[
  • 1,088 cases
  • , 828 controls
]
 Asian unspecified MVP

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
PPM014820 PSS009901|
Multi-ancestry (including European)|
45,007 individuals
 PGP000341 |
Vujkovic M et al. Nat Genet (2022)
 Reported Trait: Non-alcoholic fatty liver disease — — Risk difference: 0.604 [0.418, 0.79] age, gender, 3-5 ancestry PCs —
PPM022311 PSS011911|
Multi-ancestry (including European)|
48,603 individuals
 PGP000701 |
Loesch DP et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: non-alcoholic fattly liver disease OR: 1.31 [1.21, 1.41] — — age, age^2, sex, UKB centre, array, genetic PCS 1-20 —
PPM022322 PSS011912|
European Ancestry|
45,356 individuals
 PGP000701 |
Loesch DP et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: non-alcoholic fattly liver disease OR: 1.31 [1.21, 1.42] — — age, age^2, sex, UKB centre, array, genetic PCS 1-20 —

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
PSS011911 ICD10: E11 for T2D, N18 for CKD, first occurence of I20-125 for CAD. BMI: baseline body mass index Median = 14.8 years 48,603 individuals,
46.0 % Male samples
 Mean = 56.8 years
Sd = 8.2 years		 European, East Asian, South Asian, Hispanic or Latin American, African unspecified — UKB —
PSS011912 ICD10: E11 for T2D, N18 for CKD, first occurence of I20-125 for CAD, K76.0 for NAFLD. BMI: baseline body mass index Median = 14.8 years 45,356 individuals,
46.0 % Male samples
 Mean = 57.1 years
Sd = 8.1 years		 European — UKB —
PSS009901 — —
[
  • 2,829 cases
  • , 41,391 controls
]
 — European U.S. BioVU, CAP, EPOS PIVENS, FLINT, NASH
PSS009901 — —
[
  • 444 cases
  • , 343 controls
]
 — Hispanic or Latin American U.S. NR LQTS, NASH