Polygenic Score (PGS) ID: PGS000680

Predicted Trait
Reported Trait Cystatin C [mg/L]
Mapped Trait(s) cystatin C measurement (EFO_0004617)
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.Cystatin_C
Variants
Original Genome Build hg19
Number of Variants 24,487
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)

Contributing Samples

Score Development/Training
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
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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM001408 PSS000677 PGP000128
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.17697
Spearman's ρ: 0.196
Age, sex, PCs(1-40)
PPM001443 PSS000678 PGP000128
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.28853
Spearman's ρ: 0.274
Age, sex, PCs(1-40)
PPM001478 PSS000679 PGP000128
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.30498
Spearman's ρ: 0.391
Age, sex, PCs(1-40)
PPM001513 PSS000680 PGP000128
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.26742
Spearman's ρ: 0.323
Age, sex, PCs(1-40)
PPM001548 PSS000681 PGP000128
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] : 0.29509
Spearman's ρ: 0.405
Age, sex, PCs(1-40)
PPM001591 PSS000802 PGP000128
Sinnott-Armstrong N et al. Nat Genet (2021)
Reported Trait: Cystatin C [mg/L] Spearman's ρ: 0.255 Age, sex

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000679 23,580 individuals European Non-British White UKB
PSS000680 7,338 individuals South Asian UKB
PSS000681 63,762 individuals European
(British)
UKB
PSS000802 2,116 individuals European Participants self-identifying as white MESA
PSS000677 6,015 individuals African unspecified UKB
PSS000678 1,082 individuals East Asian UKB