Trait: serum alanine aminotransferase measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004735
Description
  • Is a quantification of serum alanine aminotransferase, most commonly found in liver, the test is used in ascertainment of liver function.
Trait category
Liver enzyme measurement
Synonyms 2 synonyms
  • alanine aminotransferase measurement
  • alanine transaminase measurement
Mapped term(s) 2 mapped terms
  • NCIt:C61017
  • SNOMEDCT:34608000

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000668
(snpnet.Alanine_aminotransferase)
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Alanine aminotransferase [U/L] serum alanine aminotransferase measurement 12,076
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http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000668/ScoringFiles/PGS000668.txt.gz - Check Terms/Licenses

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)
Evaluated Score 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
PPM001431 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000623|
East Asian Ancestry|
1,081 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.1561
Spearman's ρ: 0.145
Age, sex, PCs(1-40)
PPM001396 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000622|
African Ancestry|
6,017 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.17646
Spearman's ρ: 0.092
Age, sex, PCs(1-40)
PPM001536 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000626|
European Ancestry|
63,766 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.19165
Spearman's ρ: 0.244
Age, sex, PCs(1-40)
PPM001501 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000625|
South Asian Ancestry|
7,325 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.18304
Spearman's ρ: 0.198
Age, sex, PCs(1-40)
PPM001466 PGS000668
(snpnet.Alanine_aminotransferase)
PSS000624|
European Ancestry|
23,569 individuals
PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Alanine aminotransferase [U/L] : 0.2041
Spearman's ρ: 0.22
Age, sex, PCs(1-40)

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