Trait: musculoskeletal system benign neoplasm

Trait Information
Identifier MONDO_0000636
Description A benign neoplasm that involves the musculoskeletal system. [MONDO: patterns/location]
Trait category
Other trait
Synonym musculoskeletal system benign neoplasm
Child trait(s) uterine corpus leiomyoma

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 "musculoskeletal 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)
PGS001032
(GBE_HC31)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Uterine fibroids uterine corpus leiomyoma 161
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001032/ScoringFiles/PGS001032.txt.gz
PGS002263
(PRS_UF)
 PGP000291 |
Piekos JA et al. Hum Genet (2022)
 Uterine fibroids uterine corpus leiomyoma 4,457
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002263/ScoringFiles/PGS002263.txt.gz
PGS018625
(TPMI_218.1_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Uterine leiomyoma uterine corpus leiomyoma 2,512
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018625/ScoringFiles/PGS018625.txt.gz
PGS018626
(TPMI_218.1_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Uterine leiomyoma uterine corpus leiomyoma 270,998
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018626/ScoringFiles/PGS018626.txt.gz
PGS018627
(TPMI_218.1_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Uterine leiomyoma uterine corpus leiomyoma 34,428
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018627/ScoringFiles/PGS018627.txt.gz
PGS018628
(TPMI_218.1_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Uterine leiomyoma uterine corpus leiomyoma 983,780
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018628/ScoringFiles/PGS018628.txt.gz
PGS018629
(TPMI_218.1_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Uterine leiomyoma uterine corpus leiomyoma 976,959
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018629/ScoringFiles/PGS018629.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
PPM007923 PGS001032
(GBE_HC31)
 PSS004432|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Uterine fibroids — AUROC: 0.76646 [0.74986, 0.78306] R²: 0.19353
Incremental AUROC (full-covars): 0.00769
PGS R2 (no covariates): 0.00167
PGS AUROC (no covariates): 0.52708 [0.49761, 0.55655]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007924 PGS001032
(GBE_HC31)
 PSS004433|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Uterine fibroids — AUROC: 0.78861 [0.72118, 0.85605] R²: 0.15287
Incremental AUROC (full-covars): -0.00776
PGS R2 (no covariates): 2e-05
PGS AUROC (no covariates): 0.48768 [0.36905, 0.60631]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007925 PGS001032
(GBE_HC31)
 PSS004434|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Uterine fibroids — AUROC: 0.76622 [0.75066, 0.78178] R²: 0.12754
Incremental AUROC (full-covars): 0.00896
PGS R2 (no covariates): 0.00275
PGS AUROC (no covariates): 0.54817 [0.52052, 0.57581]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007926 PGS001032
(GBE_HC31)
 PSS004435|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Uterine fibroids — AUROC: 0.84627 [0.82086, 0.87168] R²: 0.18068
Incremental AUROC (full-covars): 0.00364
PGS R2 (no covariates): 0.00384
PGS AUROC (no covariates): 0.55148 [0.49383, 0.60912]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007927 PGS001032
(GBE_HC31)
 PSS004436|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Uterine fibroids — AUROC: 0.78165 [0.77294, 0.79036] R²: 0.14246
Incremental AUROC (full-covars): 0.00535
PGS R2 (no covariates): 0.00214
PGS AUROC (no covariates): 0.54273 [0.52605, 0.55942]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM012882 PGS002263
(PRS_UF)
 PSS009591|
European Ancestry|
26,637 individuals
 PGP000291 |
Piekos JA et al. Hum Genet (2022)
 Reported Trait: Uterine fibroid OR: 1.35 [1.34, 1.37] AUROC: 0.6 [0.58, 0.62] — BMI, age, 10 principal components —
PPM012883 PGS002263
(PRS_UF)
 PSS009591|
European Ancestry|
26,637 individuals
 PGP000291 |
Piekos JA et al. Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus OR: 1.31 [1.26, 1.37] — — BMI, age, 10 principal components —
PPM012884 PGS002263
(PRS_UF)
 PSS009591|
European Ancestry|
26,637 individuals
 PGP000291 |
Piekos JA et al. Hum Genet (2022)
 Reported Trait: Uterine leiomyoma OR: 1.32 [1.26, 1.37] — — BMI, age, 10 principal components —
PPM036807 PGS018625
(TPMI_218.1_Lassosum2)
 PSS012523|
East Asian Ancestry|
9,417 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Uterine leiomyoma — AUROC: 0.83022 R²: 0.23694 sex, age, array, PCs 1-10 —
PPM036808 PGS018626
(TPMI_218.1_LDpred2)
 PSS012522|
East Asian Ancestry|
9,417 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Uterine leiomyoma — AUROC: 0.83104 R²: 0.23821 sex, age, array, PCs 1-10 —
PPM036809 PGS018627
(TPMI_218.1_MegaPRS)
 PSS012524|
East Asian Ancestry|
9,417 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Uterine leiomyoma — AUROC: 0.83009 R²: 0.23677 sex, age, array, PCs 1-10 —
PPM036810 PGS018628
(TPMI_218.1_PRS-CS)
 PSS012525|
East Asian Ancestry|
9,417 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Uterine leiomyoma — AUROC: 0.83054 R²: 0.23802 sex, age, array, PCs 1-10 —
PPM036811 PGS018629
(TPMI_218.1_SBayesR)
 PSS012526|
East Asian Ancestry|
9,417 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Uterine leiomyoma — AUROC: 0.83004 R²: 0.23693 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
PSS009591 — — 26,637 individuals,
0.0 % Male samples
 Mean = 67.04 years
Sd = 19.14 years		 European
(White)		 — eMERGE —
PSS012522 218,D25 —
[
  • 938 cases
  • , 8,479 controls
]
,
0.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012523 218,D25 —
[
  • 938 cases
  • , 8,479 controls
]
,
0.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012524 218,D25 —
[
  • 938 cases
  • , 8,479 controls
]
,
0.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012525 218,D25 —
[
  • 938 cases
  • , 8,479 controls
]
,
0.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012526 218,D25 —
[
  • 938 cases
  • , 8,479 controls
]
,
0.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS004432 — —
[
  • 389 cases
  • , 6,108 controls
]
 — African unspecified — UKB —
PSS004433 — —
[
  • 28 cases
  • , 1,676 controls
]
 — East Asian — UKB —
PSS004434 — —
[
  • 406 cases
  • , 24,499 controls
]
 — European non-white British ancestry UKB —
PSS004435 — —
[
  • 88 cases
  • , 7,743 controls
]
 — South Asian — UKB —
PSS004436 — —
[
  • 1,148 cases
  • , 66,277 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)