Trait: benign endocrine neoplasm

Trait Information
Identifier MONDO_0000627
Description A non-metastasizing, functioning or non-functioning neoplasm that arises from an endocrine organ. Representative examples include thyroid gland follicular adenoma and parathyroid gland adenoma. [NCIT: C4621]
Trait category
Other trait
Synonyms 13 synonyms
  • benign endocrine gland neoplasm
  • benign endocrine gland tumor
  • benign endocrine gland tumour
  • benign endocrine neoplasm
  • benign endocrine tumor
  • benign endocrine tumour
  • benign neoplasm of endocrine gland
  • benign neoplasm of the endocrine gland
  • benign tumor of endocrine gland
  • benign tumor of the endocrine gland
  • benign tumour of endocrine gland
  • benign tumour of the endocrine gland
  • endocrine gland benign neoplasm
Child trait(s) benign thyroid gland 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 "benign endocrine 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)
PGS018635
(TPMI_226_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of thyroid glands benign thyroid gland neoplasm 90
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018635/ScoringFiles/PGS018635.txt.gz
PGS018636
(TPMI_226_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of thyroid glands benign thyroid gland neoplasm 310,396
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018636/ScoringFiles/PGS018636.txt.gz
PGS018637
(TPMI_226_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of thyroid glands benign thyroid gland neoplasm 499,454
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018637/ScoringFiles/PGS018637.txt.gz
PGS018638
(TPMI_226_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of thyroid glands benign thyroid gland neoplasm 983,834
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018638/ScoringFiles/PGS018638.txt.gz
PGS018639
(TPMI_226_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of thyroid glands benign thyroid gland neoplasm 1,003,044
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018639/ScoringFiles/PGS018639.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
PPM036817 PGS018635
(TPMI_226_Lassosum2)
 PSS012538|
East Asian Ancestry|
19,294 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of thyroid glands — AUROC: 0.71775 R²: 0.01182 sex, age, array, PCs 1-10 —
PPM036818 PGS018636
(TPMI_226_LDpred2)
 PSS012537|
East Asian Ancestry|
19,294 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of thyroid glands — AUROC: 0.72037 R²: 0.0121 sex, age, array, PCs 1-10 —
PPM036819 PGS018637
(TPMI_226_MegaPRS)
 PSS012539|
East Asian Ancestry|
19,294 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of thyroid glands — AUROC: 0.71459 R²: 0.01105 sex, age, array, PCs 1-10 —
PPM036820 PGS018638
(TPMI_226_PRS-CS)
 PSS012540|
East Asian Ancestry|
19,294 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of thyroid glands — AUROC: 0.71768 R²: 0.01154 sex, age, array, PCs 1-10 —
PPM036821 PGS018639
(TPMI_226_SBayesR)
 PSS012541|
East Asian Ancestry|
19,294 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of thyroid glands — AUROC: 0.7189 R²: 0.01135 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
PSS012541 226,D34 —
[
  • 155 cases
  • , 19,139 controls
]
,
46.52 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012537 226,D34 —
[
  • 155 cases
  • , 19,139 controls
]
,
46.52 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012538 226,D34 —
[
  • 155 cases
  • , 19,139 controls
]
,
46.52 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012539 226,D34 —
[
  • 155 cases
  • , 19,139 controls
]
,
46.52 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012540 226,D34 —
[
  • 155 cases
  • , 19,139 controls
]
,
46.52 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —