Trait: integumentary system benign neoplasm

Trait Information
Identifier MONDO_0000652
Description A benign neoplasm that involves the integumental system. [MONDO: patterns/location]
Trait category
Other trait
Synonym integumental system benign neoplasm
Child trait(s) common wart

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:
Display options:
Ancestry legend
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
Note: This table shows PGS for child terms of "integumentary system benign neoplasm" in the EFO hierarchy.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001011
(GBE_HC534)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Viral warts (time-to-event) common wart 5
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001011/ScoringFiles/PGS001011.txt.gz
PGS018440
(TPMI_078_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Viral warts HPV common wart 85
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018440/ScoringFiles/PGS018440.txt.gz
PGS018441
(TPMI_078_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Viral warts HPV common wart 939,884
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018441/ScoringFiles/PGS018441.txt.gz
PGS018442
(TPMI_078_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Viral warts HPV common wart 21,918
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018442/ScoringFiles/PGS018442.txt.gz
PGS018443
(TPMI_078_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Viral warts HPV common wart 983,817
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018443/ScoringFiles/PGS018443.txt.gz
PGS018444
(TPMI_078_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Viral warts HPV common wart 978,577
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018444/ScoringFiles/PGS018444.txt.gz

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
PPM007818 PGS001011
(GBE_HC534)
 PSS004521|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.62763 [0.56904, 0.68622] R²: 0.01913
Incremental AUROC (full-covars): -0.00455
PGS R2 (no covariates): 0.00116
PGS AUROC (no covariates): 0.48242 [0.41987, 0.54497]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007819 PGS001011
(GBE_HC534)
 PSS004522|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.65545 [0.57671, 0.73418] R²: 0.03677
Incremental AUROC (full-covars): -0.00026
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.50846 [0.40705, 0.60986]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007820 PGS001011
(GBE_HC534)
 PSS004523|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.56023 [0.54032, 0.58015] R²: 0.0051
Incremental AUROC (full-covars): 0.01103
PGS R2 (no covariates): 0.00154
PGS AUROC (no covariates): 0.53437 [0.51402, 0.55472]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007821 PGS001011
(GBE_HC534)
 PSS004524|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.5793 [0.54592, 0.61268] R²: 0.01114
Incremental AUROC (full-covars): 0.00245
PGS R2 (no covariates): 0.00048
PGS AUROC (no covariates): 0.51036 [0.47743, 0.54328]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007822 PGS001011
(GBE_HC534)
 PSS004525|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE viral warts — AUROC: 0.56004 [0.54811, 0.57198] R²: 0.00576
Incremental AUROC (full-covars): 0.00636
PGS R2 (no covariates): 0.00167
PGS AUROC (no covariates): 0.53057 [0.51862, 0.54252]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM036622 PGS018440
(TPMI_078_Lassosum2)
 PSS012343|
East Asian Ancestry|
15,250 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Viral warts HPV — AUROC: 0.68328 R²: 0.05397 sex, age, array, PCs 1-10 —
PPM036623 PGS018441
(TPMI_078_LDpred2)
 PSS012342|
East Asian Ancestry|
15,250 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Viral warts HPV — AUROC: 0.68573 R²: 0.05489 sex, age, array, PCs 1-10 —
PPM036624 PGS018442
(TPMI_078_MegaPRS)
 PSS012344|
East Asian Ancestry|
15,250 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Viral warts HPV — AUROC: 0.68774 R²: 0.05587 sex, age, array, PCs 1-10 —
PPM036625 PGS018443
(TPMI_078_PRS-CS)
 PSS012345|
East Asian Ancestry|
15,250 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Viral warts HPV — AUROC: 0.69124 R²: 0.05719 sex, age, array, PCs 1-10 —
PPM036626 PGS018444
(TPMI_078_SBayesR)
 PSS012346|
East Asian Ancestry|
15,250 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Viral warts HPV — AUROC: 0.68781 R²: 0.05626 sex, age, array, PCs 1-10 —

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
PSS004521 — —
[
  • 81 cases
  • , 6,416 controls
]
 — African unspecified — UKB —
PSS004522 — —
[
  • 32 cases
  • , 1,672 controls
]
 — East Asian — UKB —
PSS004523 — —
[
  • 781 cases
  • , 24,124 controls
]
 — European non-white British ancestry UKB —
PSS004524 — —
[
  • 307 cases
  • , 7,524 controls
]
 — South Asian — UKB —
PSS004525 — —
[
  • 2,358 cases
  • , 65,067 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS012342 078.1, 079.4,A63.0, B07, B97.7 —
[
  • 339 cases
  • , 14,911 controls
]
,
45.03 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012343 078.1, 079.4,A63.0, B07, B97.7 —
[
  • 339 cases
  • , 14,911 controls
]
,
45.03 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012344 078.1, 079.4,A63.0, B07, B97.7 —
[
  • 339 cases
  • , 14,911 controls
]
,
45.03 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012345 078.1, 079.4,A63.0, B07, B97.7 —
[
  • 339 cases
  • , 14,911 controls
]
,
45.03 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012346 078.1, 079.4,A63.0, B07, B97.7 —
[
  • 339 cases
  • , 14,911 controls
]
,
45.03 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —