Trait: benign female reproductive system neoplasm

Trait Information
Identifier MONDO_0000624
Description A non-metastasizing neoplasm that arises from the female reproductive system. Representative examples include uterine corpus leiomyoma, endocervical polyp, and benign ovarian germ cell tumor. [NCIT: C4934]
Trait category
Other trait
Synonyms 7 synonyms
  • benign female reproductive system neoplasm
  • benign female reproductive system tumor
  • benign female reproductive system tumour
  • benign gynecologic neoplasm
  • benign gynecologic tumor
  • benign gynecologic tumour
  • female reproductive organ benign neoplasm
Child trait(s) 2 child traits

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 "benign female reproductive system 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
PGS001813
(portability-PLR_218)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Benign neoplasm of uterus uterine benign neoplasm 1,308
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001813/ScoringFiles/PGS001813.txt.gz
PGS002021
(portability-ldpred2_218)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Benign neoplasm of uterus uterine benign neoplasm 547,617
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002021/ScoringFiles/PGS002021.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
PGS018620
(TPMI_218_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of uterus uterine benign neoplasm 222
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018620/ScoringFiles/PGS018620.txt.gz
PGS018621
(TPMI_218_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of uterus uterine benign neoplasm 939,827
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018621/ScoringFiles/PGS018621.txt.gz
PGS018622
(TPMI_218_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of uterus uterine benign neoplasm 32,529
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018622/ScoringFiles/PGS018622.txt.gz
PGS018623
(TPMI_218_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of uterus uterine benign neoplasm 983,782
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018623/ScoringFiles/PGS018623.txt.gz
PGS018624
(TPMI_218_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of uterus uterine benign neoplasm 982,615
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018624/ScoringFiles/PGS018624.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
PPM009404 PGS001813
(portability-PLR_218)
 PSS009283|
European Ancestry|
10,254 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0392 [0.0199, 0.0586] sex, age, birth date, deprivation index, 16 PCs —
PPM009405 PGS001813
(portability-PLR_218)
 PSS009057|
European Ancestry|
2,468 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0775 [0.038, 0.1168] sex, age, birth date, deprivation index, 16 PCs —
PPM009406 PGS001813
(portability-PLR_218)
 PSS008611|
European Ancestry|
3,518 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0381 [0.005, 0.0712] sex, age, birth date, deprivation index, 16 PCs —
PPM009407 PGS001813
(portability-PLR_218)
 PSS008387|
Greater Middle Eastern Ancestry|
467 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.1251 [0.0328, 0.2152] sex, age, birth date, deprivation index, 16 PCs —
PPM009408 PGS001813
(portability-PLR_218)
 PSS008165|
South Asian Ancestry|
2,817 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0862 [0.0493, 0.1228] sex, age, birth date, deprivation index, 16 PCs —
PPM009409 PGS001813
(portability-PLR_218)
 PSS007952|
East Asian Ancestry|
1,164 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0245 [-0.0335, 0.0823] sex, age, birth date, deprivation index, 16 PCs —
PPM009410 PGS001813
(portability-PLR_218)
 PSS007733|
African Ancestry|
1,520 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0263 [-0.0244, 0.0768] sex, age, birth date, deprivation index, 16 PCs —
PPM009411 PGS001813
(portability-PLR_218)
 PSS008836|
African Ancestry|
2,067 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0186 [-0.0248, 0.0618] sex, age, birth date, deprivation index, 16 PCs —
PPM011042 PGS002021
(portability-ldpred2_218)
 PSS009283|
European Ancestry|
10,254 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0479 [0.0286, 0.0672] sex, age, birth date, deprivation index, 16 PCs —
PPM011043 PGS002021
(portability-ldpred2_218)
 PSS009057|
European Ancestry|
2,468 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.1046 [0.0653, 0.1436] sex, age, birth date, deprivation index, 16 PCs —
PPM011044 PGS002021
(portability-ldpred2_218)
 PSS008611|
European Ancestry|
3,518 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0454 [0.0123, 0.0785] sex, age, birth date, deprivation index, 16 PCs —
PPM011046 PGS002021
(portability-ldpred2_218)
 PSS008165|
South Asian Ancestry|
2,817 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0966 [0.0597, 0.1332] sex, age, birth date, deprivation index, 16 PCs —
PPM011048 PGS002021
(portability-ldpred2_218)
 PSS007733|
African Ancestry|
1,520 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0301 [-0.0205, 0.0806] sex, age, birth date, deprivation index, 16 PCs —
PPM011045 PGS002021
(portability-ldpred2_218)
 PSS008387|
Greater Middle Eastern Ancestry|
467 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.152 [0.0602, 0.2413] sex, age, birth date, deprivation index, 16 PCs —
PPM011047 PGS002021
(portability-ldpred2_218)
 PSS007952|
East Asian Ancestry|
1,164 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0232 [-0.0347, 0.0811] sex, age, birth date, deprivation index, 16 PCs —
PPM011049 PGS002021
(portability-ldpred2_218)
 PSS008836|
African Ancestry|
2,067 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of uterus — — Partial Correlation (partial-r): 0.0238 [-0.0195, 0.067] sex, age, birth date, deprivation index, 16 PCs —
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 —
PPM036802 PGS018620
(TPMI_218_Lassosum2)
 PSS012528|
East Asian Ancestry|
9,554 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of uterus — AUROC: 0.82762 R²: 0.2413 sex, age, array, PCs 1-10 —
PPM036803 PGS018621
(TPMI_218_LDpred2)
 PSS012527|
East Asian Ancestry|
9,554 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of uterus — AUROC: 0.8279 R²: 0.2419 sex, age, array, PCs 1-10 —
PPM036804 PGS018622
(TPMI_218_MegaPRS)
 PSS012529|
East Asian Ancestry|
9,554 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of uterus — AUROC: 0.82717 R²: 0.24082 sex, age, array, PCs 1-10 —
PPM036805 PGS018623
(TPMI_218_PRS-CS)
 PSS012530|
East Asian Ancestry|
9,554 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of uterus — AUROC: 0.82812 R²: 0.24235 sex, age, array, PCs 1-10 —
PPM036806 PGS018624
(TPMI_218_SBayesR)
 PSS012531|
East Asian Ancestry|
9,554 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of uterus — AUROC: 0.82824 R²: 0.24295 sex, age, array, PCs 1-10 —
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
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)
PSS009057 — — 2,468 individuals — European Poland (NE Europe) UKB —
PSS008165 — — 2,817 individuals — South Asian India (South Asia) UKB —
PSS009591 — — 26,637 individuals,
0.0 % Male samples
 Mean = 67.04 years
Sd = 19.14 years		 European
(White)		 — eMERGE —
PSS009283 — — 10,254 individuals — European UK (+ Ireland) UKB —
PSS008836 — — 2,067 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007952 — — 1,164 individuals — East Asian China (East Asia) UKB —
PSS008611 — — 3,518 individuals — European Italy (South Europe) UKB —
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 —
PSS007733 — — 1,520 individuals — African American or Afro-Caribbean Carribean UKB —
PSS012527 218, 219,D25, D26 —
[
  • 1,075 cases
  • , 8,479 controls
]
,
0.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012528 218, 219,D25, D26 —
[
  • 1,075 cases
  • , 8,479 controls
]
,
0.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012529 218, 219,D25, D26 —
[
  • 1,075 cases
  • , 8,479 controls
]
,
0.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012530 218, 219,D25, D26 —
[
  • 1,075 cases
  • , 8,479 controls
]
,
0.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012531 218, 219,D25, D26 —
[
  • 1,075 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 —
PSS008387 — — 467 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —