Trait: intestinal benign neoplasm

Trait Information
Identifier MONDO_0003062
Description A benign neoplasm that involves the intestine. [MONDO: patterns/location]
Trait categories
Digestive system disorder
Other disease
Synonyms 20 synonyms
  • benign intestinal neoplasm
  • benign intestinal neoplasms
  • benign intestinal tumor
  • benign intestinal tumors
  • benign intestinal tumour
  • benign intestinal tumours
  • benign intestine neoplasm
  • benign intestine tumor
  • benign intestine tumour
  • benign neoplasm of intestines
  • benign neoplasm of the intestines
  • benign neoplasms of large and/or small intestine
  • benign neoplasms of the large and/or small intestine
  • benign tumor of intestines
  • benign tumor of the intestines
  • benign tumour of intestines
  • benign tumour of the intestines
  • intestinal neoplasms, benign
  • intestinal tumors, benign
  • intestine benign neoplasm
Child trait(s) benign colon neoplasm

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 "intestinal 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)
PGS001811
(portability-PLR_208)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Benign neoplasm of colon benign colon neoplasm 2,231
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001811/ScoringFiles/PGS001811.txt.gz
PGS002019
(portability-ldpred2_208)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Benign neoplasm of colon benign colon neoplasm 667,546
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002019/ScoringFiles/PGS002019.txt.gz
PGS018610
(TPMI_208_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of colon benign colon neoplasm 1,006
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018610/ScoringFiles/PGS018610.txt.gz
PGS018611
(TPMI_208_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of colon benign colon neoplasm 939,899
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018611/ScoringFiles/PGS018611.txt.gz
PGS018612
(TPMI_208_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of colon benign colon neoplasm 474,603
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018612/ScoringFiles/PGS018612.txt.gz
PGS018613
(TPMI_208_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of colon benign colon neoplasm 983,832
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018613/ScoringFiles/PGS018613.txt.gz
PGS018614
(TPMI_208_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of colon benign colon neoplasm 933,825
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018614/ScoringFiles/PGS018614.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
PPM009388 PGS001811
(portability-PLR_208)
 PSS009281|
European Ancestry|
19,812 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0643 [0.0504, 0.0782] sex, age, birth date, deprivation index, 16 PCs —
PPM009389 PGS001811
(portability-PLR_208)
 PSS009055|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0651 [0.0345, 0.0955] sex, age, birth date, deprivation index, 16 PCs —
PPM009390 PGS001811
(portability-PLR_208)
 PSS008609|
European Ancestry|
6,617 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0584 [0.0343, 0.0824] sex, age, birth date, deprivation index, 16 PCs —
PPM009391 PGS001811
(portability-PLR_208)
 PSS008385|
Greater Middle Eastern Ancestry|
1,194 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0914 [0.0344, 0.1478] sex, age, birth date, deprivation index, 16 PCs —
PPM009392 PGS001811
(portability-PLR_208)
 PSS008163|
South Asian Ancestry|
6,307 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.023 [-0.0017, 0.0477] sex, age, birth date, deprivation index, 16 PCs —
PPM009393 PGS001811
(portability-PLR_208)
 PSS007950|
East Asian Ancestry|
1,800 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0293 [-0.0171, 0.0757] sex, age, birth date, deprivation index, 16 PCs —
PPM009394 PGS001811
(portability-PLR_208)
 PSS007731|
African Ancestry|
2,469 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0518 [0.0122, 0.0912] sex, age, birth date, deprivation index, 16 PCs —
PPM009395 PGS001811
(portability-PLR_208)
 PSS008834|
African Ancestry|
3,905 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0459 [0.0145, 0.0772] sex, age, birth date, deprivation index, 16 PCs —
PPM011026 PGS002019
(portability-ldpred2_208)
 PSS009281|
European Ancestry|
19,812 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0716 [0.0577, 0.0854] sex, age, birth date, deprivation index, 16 PCs —
PPM011027 PGS002019
(portability-ldpred2_208)
 PSS009055|
European Ancestry|
4,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0761 [0.0456, 0.1065] sex, age, birth date, deprivation index, 16 PCs —
PPM011028 PGS002019
(portability-ldpred2_208)
 PSS008609|
European Ancestry|
6,617 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0659 [0.0418, 0.0899] sex, age, birth date, deprivation index, 16 PCs —
PPM011029 PGS002019
(portability-ldpred2_208)
 PSS008385|
Greater Middle Eastern Ancestry|
1,194 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0966 [0.0396, 0.153] sex, age, birth date, deprivation index, 16 PCs —
PPM011030 PGS002019
(portability-ldpred2_208)
 PSS008163|
South Asian Ancestry|
6,307 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0398 [0.0151, 0.0645] sex, age, birth date, deprivation index, 16 PCs —
PPM011031 PGS002019
(portability-ldpred2_208)
 PSS007950|
East Asian Ancestry|
1,800 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0601 [0.0137, 0.1063] sex, age, birth date, deprivation index, 16 PCs —
PPM011032 PGS002019
(portability-ldpred2_208)
 PSS007731|
African Ancestry|
2,469 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0409 [0.0012, 0.0803] sex, age, birth date, deprivation index, 16 PCs —
PPM011033 PGS002019
(portability-ldpred2_208)
 PSS008834|
African Ancestry|
3,905 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of colon — — Partial Correlation (partial-r): 0.0603 [0.0289, 0.0916] sex, age, birth date, deprivation index, 16 PCs —
PPM036792 PGS018610
(TPMI_208_Lassosum2)
 PSS012513|
East Asian Ancestry|
18,707 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of colon — AUROC: 0.594 R²: 0.02719 sex, age, array, PCs 1-10 —
PPM036793 PGS018611
(TPMI_208_LDpred2)
 PSS012512|
East Asian Ancestry|
18,707 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of colon — AUROC: 0.59584 R²: 0.02821 sex, age, array, PCs 1-10 —
PPM036794 PGS018612
(TPMI_208_MegaPRS)
 PSS012514|
East Asian Ancestry|
18,707 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of colon — AUROC: 0.59631 R²: 0.02871 sex, age, array, PCs 1-10 —
PPM036795 PGS018613
(TPMI_208_PRS-CS)
 PSS012515|
East Asian Ancestry|
18,707 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of colon — AUROC: 0.59443 R²: 0.02741 sex, age, array, PCs 1-10 —
PPM036796 PGS018614
(TPMI_208_SBayesR)
 PSS012516|
East Asian Ancestry|
18,707 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of colon — AUROC: 0.59494 R²: 0.02796 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
PSS012512 209.5, 211.3, 211.4, V12.72,D12, D3A, K63.5, Z86.010 —
[
  • 1,308 cases
  • , 17,399 controls
]
,
45.56 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012513 209.5, 211.3, 211.4, V12.72,D12, D3A, K63.5, Z86.010 —
[
  • 1,308 cases
  • , 17,399 controls
]
,
45.56 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012514 209.5, 211.3, 211.4, V12.72,D12, D3A, K63.5, Z86.010 —
[
  • 1,308 cases
  • , 17,399 controls
]
,
45.56 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012515 209.5, 211.3, 211.4, V12.72,D12, D3A, K63.5, Z86.010 —
[
  • 1,308 cases
  • , 17,399 controls
]
,
45.56 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012516 209.5, 211.3, 211.4, V12.72,D12, D3A, K63.5, Z86.010 —
[
  • 1,308 cases
  • , 17,399 controls
]
,
45.56 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS007950 — — 1,800 individuals — East Asian China (East Asia) UKB —
PSS007731 — — 2,469 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009281 — — 19,812 individuals — European UK (+ Ireland) UKB —
PSS008385 — — 1,194 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009055 — — 4,121 individuals — European Poland (NE Europe) UKB —
PSS008609 — — 6,617 individuals — European Italy (South Europe) UKB —
PSS008834 — — 3,905 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008163 — — 6,307 individuals — South Asian India (South Asia) UKB —