Polygenic Score (PGS) ID: PGS002283

Predicted Trait
Reported Trait Nonalcoholic fatty liver disease
Mapped Trait(s) non-alcoholic fatty liver disease (EFO_0003095)
Released in PGS Catalog: April 13, 2022
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Score Details

Score Construction
PGS Name GRS15_NAFLD
Development Method
Name Genome-wide significant variants
Parameters p<5E-08, MAF>1%, INFO>0.7, r2>0.8; externally validated to associate with histologically or imaging-defined NAFLD
Variants
Original Genome Build GRCh37
Number of Variants 15
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000312
Citation (link to publication) Schnurr TM et al. Hepatol Commun (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
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 68,725 cases
  • , 95,472 controls
]
 European MVP
[
  • 13,387 cases
  • , 23,977 controls
]
 African American or Afro-Caribbean MVP
[
  • 7,468 cases
  • , 7,650 controls
]
 Hispanic or Latin American MVP
[
  • 828 cases
  • , 1,088 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
PPM012974 PSS009638|
European Ancestry|
25,716 individuals
 PGP000312 |
Schnurr TM et al. Hepatol Commun (2022)
 Reported Trait: ALT levels β: 0.094 (0.002) — — — —
PPM012978 PSS009638|
European Ancestry|
25,716 individuals
 PGP000312 |
Schnurr TM et al. Hepatol Commun (2022)
 Reported Trait: ALT levels x physical activity interaction β: -0.3 (0.053) — — — —
PPM012979 PSS009638|
European Ancestry|
25,716 individuals
 PGP000312 |
Schnurr TM et al. Hepatol Commun (2022)
 Reported Trait: ALT levels x grip strength interaction β: -0.011 (0.002) — — — —
PPM012980 PSS009638|
European Ancestry|
25,716 individuals
 PGP000312 |
Schnurr TM et al. Hepatol Commun (2022)
 Reported Trait: ALT levels x BMI interaction β: 0.039 (0.002) — — — —

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
PSS009638 — — 25,716 individuals,
41.5 % Male samples
 Mean = 56.0 years
Sd = 7.7 years		 European — UKB —