Polygenic Score (PGS) ID: PGS000668

Predicted Trait
Reported Trait Alanine aminotransferase [U/L]
Mapped Trait(s) serum alanine aminotransferase measurement (EFO_0004735)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Alanine_aminotransferase
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 12,076
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
10 Sample Sets

Development Samples

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
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001466 PSS000624|
European Ancestry|
23,569 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Alanine aminotransferase [U/L] — — R²: 0.2041
Spearman's ρ: 0.22		 Age, sex, PCs(1-40) —
PPM001501 PSS000625|
South Asian Ancestry|
7,325 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Alanine aminotransferase [U/L] — — R²: 0.18304
Spearman's ρ: 0.198		 Age, sex, PCs(1-40) —
PPM001536 PSS000626|
European Ancestry|
63,766 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Alanine aminotransferase [U/L] — — R²: 0.19165
Spearman's ρ: 0.244		 Age, sex, PCs(1-40) —
PPM001396 PSS000622|
African Ancestry|
6,017 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Alanine aminotransferase [U/L] — — R²: 0.17646
Spearman's ρ: 0.092		 Age, sex, PCs(1-40) —
PPM001431 PSS000623|
East Asian Ancestry|
1,081 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Alanine aminotransferase [U/L] — — R²: 0.1561
Spearman's ρ: 0.145		 Age, sex, PCs(1-40) —
PPM007267 PSS007078|
European Ancestry|
23,758 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Alanine aminotransferase — — R²: 0.07978 [0.07332, 0.08623]
Incremental R2 (full-covars): 0.00218
PGS R2 (no covariates): 0.03 [0.02583, 0.03418]		 age, sex, UKB array type, Genotype PCs —
PPM007265 PSS007076|
African Ancestry|
6,099 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Alanine aminotransferase — — R²: 0.0977 [0.084, 0.11141]
Incremental R2 (full-covars): 0.00077
PGS R2 (no covariates): 0.00447 [0.00124, 0.00771]		 age, sex, UKB array type, Genotype PCs —
PPM007266 PSS007077|
East Asian Ancestry|
1,615 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Alanine aminotransferase — — R²: 0.08994 [0.06408, 0.11581]
Incremental R2 (full-covars): 0.00177
PGS R2 (no covariates): 0.02382 [0.00954, 0.03809]		 age, sex, UKB array type, Genotype PCs —
PPM007268 PSS007079|
South Asian Ancestry|
7,414 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Alanine aminotransferase — — R²: 0.08504 [0.07323, 0.09685]
Incremental R2 (full-covars): 0.00213
PGS R2 (no covariates): 0.02862 [0.02135, 0.0359]		 age, sex, UKB array type, Genotype PCs —
PPM007269 PSS007080|
European Ancestry|
64,440 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Alanine aminotransferase — — R²: 0.06901 [0.06532, 0.0727]
Incremental R2 (full-covars): 0.00284
PGS R2 (no covariates): 0.03994 [0.03705, 0.04284]		 age, sex, UKB array type, Genotype PCs —

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
PSS000622 — — 6,017 individuals — African unspecified — UKB —
PSS000623 — — 1,081 individuals — East Asian — UKB —
PSS000624 — — 23,569 individuals — European Non-British White UKB —
PSS000625 — — 7,325 individuals — South Asian — UKB —
PSS000626 — — 63,766 individuals — European
(British)		 — UKB —
PSS007078 — — 23,758 individuals — European non-white British ancestry UKB —
PSS007076 — — 6,099 individuals — African unspecified — UKB —
PSS007077 — — 1,615 individuals — East Asian — UKB —
PSS007079 — — 7,414 individuals — South Asian — UKB —
PSS007080 — — 64,440 individuals — European white British ancestry UKB Testing cohort (heldout set)