Trait: nervous system benign neoplasm

Trait Information
Identifier MONDO_0000648
Description Abnormal growth of cells in the nervous system without evidence of malignant characteristics. Unlike other organ systems, tumors in the central nervous system can have benign histological characteristics but still have life threatening effects due to their location within the neuraxis (e.g., brainstem gliomas). [NCIT: P378]
Trait category
Other trait
Synonyms 11 synonyms
  • benign neoplasm of nervous system
  • benign neoplasm of the nervous system
  • benign nervous system neoplasm
  • benign nervous system tumor
  • benign nervous system tumour
  • benign tumor of nervous system
  • benign tumor of the nervous system
  • benign tumour of nervous system
  • benign tumour of the nervous system
  • nervous system benign neoplasm
  • nervous system neoplasm, benign
Child trait(s) benign neoplasm of peripheral nervous system

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 "nervous 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)
PGS018630
(TPMI_225_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of brain and other parts of nervous system benign neoplasm of peripheral nervous system 105,501
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018630/ScoringFiles/PGS018630.txt.gz
PGS018631
(TPMI_225_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of brain and other parts of nervous system benign neoplasm of peripheral nervous system 939,890
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018631/ScoringFiles/PGS018631.txt.gz
PGS018632
(TPMI_225_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of brain and other parts of nervous system benign neoplasm of peripheral nervous system 18,584
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018632/ScoringFiles/PGS018632.txt.gz
PGS018633
(TPMI_225_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of brain and other parts of nervous system benign neoplasm of peripheral nervous system 983,826
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018633/ScoringFiles/PGS018633.txt.gz
PGS018634
(TPMI_225_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Benign neoplasm of brain and other parts of nervous system benign neoplasm of peripheral nervous system 994,892
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018634/ScoringFiles/PGS018634.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
PPM036812 PGS018630
(TPMI_225_Lassosum2)
 PSS012533|
East Asian Ancestry|
19,663 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of brain and other parts of nervous system — AUROC: 0.66017 R²: 0.00803 sex, age, array, PCs 1-10 —
PPM036813 PGS018631
(TPMI_225_LDpred2)
 PSS012532|
East Asian Ancestry|
19,663 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of brain and other parts of nervous system — AUROC: 0.66156 R²: 0.00841 sex, age, array, PCs 1-10 —
PPM036814 PGS018632
(TPMI_225_MegaPRS)
 PSS012534|
East Asian Ancestry|
19,663 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of brain and other parts of nervous system — AUROC: 0.66091 R²: 0.00806 sex, age, array, PCs 1-10 —
PPM036815 PGS018633
(TPMI_225_PRS-CS)
 PSS012535|
East Asian Ancestry|
19,663 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of brain and other parts of nervous system — AUROC: 0.65907 R²: 0.00795 sex, age, array, PCs 1-10 —
PPM036816 PGS018634
(TPMI_225_SBayesR)
 PSS012536|
East Asian Ancestry|
19,663 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Benign neoplasm of brain and other parts of nervous system — AUROC: 0.65916 R²: 0.00802 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
PSS012532 225, V12.41,D32.0, D32.1, D32.9, D33.0, D33.1, D33.2, D33.3, D33.4, D33.7, D33.9, Z86.011 —
[
  • 191 cases
  • , 19,472 controls
]
,
46.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012533 225, V12.41,D32.0, D32.1, D32.9, D33.0, D33.1, D33.2, D33.3, D33.4, D33.7, D33.9, Z86.011 —
[
  • 191 cases
  • , 19,472 controls
]
,
46.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012534 225, V12.41,D32.0, D32.1, D32.9, D33.0, D33.1, D33.2, D33.3, D33.4, D33.7, D33.9, Z86.011 —
[
  • 191 cases
  • , 19,472 controls
]
,
46.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012535 225, V12.41,D32.0, D32.1, D32.9, D33.0, D33.1, D33.2, D33.3, D33.4, D33.7, D33.9, Z86.011 —
[
  • 191 cases
  • , 19,472 controls
]
,
46.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012536 225, V12.41,D32.0, D32.1, D32.9, D33.0, D33.1, D33.2, D33.3, D33.4, D33.7, D33.9, Z86.011 —
[
  • 191 cases
  • , 19,472 controls
]
,
46.15 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —