Trait: benign digestive system neoplasm

Trait Information
Identifier MONDO_0000385
Description A non-metastasizing neoplasm arising from any part of the digestive system. [NCIT: P378]
Trait categories
Cancer
Digestive system disorder
Synonyms 30 synonyms
  • alimentary part of gastrointestinal system benign neoplasm
  • benign GI neoplasm
  • benign GI system neoplasm
  • benign GI system tumor
  • benign GI system tumour
  • benign GI tumor
  • benign GI tumour
  • benign digestive system tumor
  • benign digestive system tumour
  • benign gastrointestinal neoplasm
  • benign gastrointestinal system tumor
  • benign gastrointestinal system tumour
  • benign gastrointestinal tumor
  • benign gastrointestinal tumour
  • benign neoplasm of digestive system
  • benign neoplasm of gastrointestinal system
  • benign neoplasm of the digestive system
  • benign tumor of GI system
  • benign tumor of digestive system
  • benign tumor of gastrointestinal system
  • benign tumor of the GI system
  • benign tumor of the digestive system
  • benign tumor of the gastrointestinal system
  • benign tumour of GI system
  • benign tumour of digestive system
  • benign tumour of gastrointestinal system
  • benign tumour of the GI system
  • benign tumour of the digestive system
  • benign tumour of the gastrointestinal system
  • gastrointestinal system benign neoplasm
Mapped terms 4 mapped terms
  • DOID:0050624
  • MEDGEN:141680
  • NCIT:C4787
  • UMLS:C0497538
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 all PGS for "benign digestive system neoplasm" and any child terms of this trait in the EFO hierarchy by default.
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
PGS001812
(portability-PLR_211)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Benign neoplasm of other parts of digestive system benign digestive system neoplasm 801
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001812/ScoringFiles/PGS001812.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
PGS002020
(portability-ldpred2_211)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Benign neoplasm of other parts of digestive system benign digestive system neoplasm 503,832
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002020/ScoringFiles/PGS002020.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 —
PPM009396 PGS001812
(portability-PLR_211)
 PSS009282|
European Ancestry|
19,463 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0232 [0.0091, 0.0372] sex, age, birth date, deprivation index, 16 PCs —
PPM009397 PGS001812
(portability-PLR_211)
 PSS009056|
European Ancestry|
4,074 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0262 [-0.0045, 0.057] sex, age, birth date, deprivation index, 16 PCs —
PPM009398 PGS001812
(portability-PLR_211)
 PSS008610|
European Ancestry|
6,504 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0186 [-0.0058, 0.0429] sex, age, birth date, deprivation index, 16 PCs —
PPM009399 PGS001812
(portability-PLR_211)
 PSS008386|
Greater Middle Eastern Ancestry|
1,178 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0327 [-0.0249, 0.0902] sex, age, birth date, deprivation index, 16 PCs —
PPM009402 PGS001812
(portability-PLR_211)
 PSS007732|
African Ancestry|
2,441 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): -0.0065 [-0.0464, 0.0333] sex, age, birth date, deprivation index, 16 PCs —
PPM009403 PGS001812
(portability-PLR_211)
 PSS008835|
African Ancestry|
3,862 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0197 [-0.0119, 0.0513] sex, age, birth date, deprivation index, 16 PCs —
PPM009400 PGS001812
(portability-PLR_211)
 PSS008164|
South Asian Ancestry|
6,243 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0246 sex, age, birth date, deprivation index, 16 PCs —
PPM009401 PGS001812
(portability-PLR_211)
 PSS007951|
East Asian Ancestry|
1,772 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0436 [-0.0032, 0.0903] 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 —
PPM011034 PGS002020
(portability-ldpred2_211)
 PSS009282|
European Ancestry|
19,463 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0199 [0.0059, 0.034] sex, age, birth date, deprivation index, 16 PCs —
PPM011035 PGS002020
(portability-ldpred2_211)
 PSS009056|
European Ancestry|
4,074 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0332 [0.0025, 0.064] sex, age, birth date, deprivation index, 16 PCs —
PPM011036 PGS002020
(portability-ldpred2_211)
 PSS008610|
European Ancestry|
6,504 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0281 [0.0038, 0.0524] sex, age, birth date, deprivation index, 16 PCs —
PPM011037 PGS002020
(portability-ldpred2_211)
 PSS008386|
Greater Middle Eastern Ancestry|
1,178 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0488 [-0.0088, 0.1061] sex, age, birth date, deprivation index, 16 PCs —
PPM011038 PGS002020
(portability-ldpred2_211)
 PSS008164|
South Asian Ancestry|
6,243 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0343 [0.0094, 0.0591] sex, age, birth date, deprivation index, 16 PCs —
PPM011039 PGS002020
(portability-ldpred2_211)
 PSS007951|
East Asian Ancestry|
1,772 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0236 [-0.0233, 0.0703] sex, age, birth date, deprivation index, 16 PCs —
PPM011040 PGS002020
(portability-ldpred2_211)
 PSS007732|
African Ancestry|
2,441 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): -0.0196 [-0.0594, 0.0202] sex, age, birth date, deprivation index, 16 PCs —
PPM011041 PGS002020
(portability-ldpred2_211)
 PSS008835|
African Ancestry|
3,862 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Benign neoplasm of other parts of digestive system — — Partial Correlation (partial-r): 0.0027 [-0.0289, 0.0343] sex, age, birth date, deprivation index, 16 PCs —

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
PSS008164 — — 6,243 individuals — South Asian India (South Asia) UKB —
PSS008386 — — 1,178 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008610 — — 6,504 individuals — European Italy (South Europe) UKB —
PSS007950 — — 1,800 individuals — East Asian China (East Asia) UKB —
PSS007951 — — 1,772 individuals — East Asian China (East Asia) UKB —
PSS007731 — — 2,469 individuals — African American or Afro-Caribbean Carribean UKB —
PSS007732 — — 2,441 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008835 — — 3,862 individuals — African unspecified Nigeria (West Africa) 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 —
PSS009282 — — 19,463 individuals — European UK (+ Ireland) UKB —
PSS009055 — — 4,121 individuals — European Poland (NE Europe) UKB —
PSS009056 — — 4,074 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 —