Trait: lymphangioma

Trait Information
Identifier MONDO_0002013
Description A benign lesion composed of dilated lymphatic channels. Painless swelling is the usual clinical manifestation. [NCIT: C8965]
Trait category
Other trait
Synonyms 5 synonyms
  • LM
  • benign lymphangioma (morphologic abnormality)
  • congenital lymphangioma
  • lymphangioma
  • lymphangioma, benign

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
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)
PGS018640
(TPMI_228_Lassosum2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Hemangioma and lymphangioma any site lymphangioma,
hemangioma		 488
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018640/ScoringFiles/PGS018640.txt.gz
PGS018641
(TPMI_228_LDpred2)
 PGP000835 |
Chen HH et al. Nature (2025)
 Hemangioma and lymphangioma any site lymphangioma,
hemangioma		 939,901
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018641/ScoringFiles/PGS018641.txt.gz
PGS018642
(TPMI_228_MegaPRS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Hemangioma and lymphangioma any site lymphangioma,
hemangioma		 34,069
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018642/ScoringFiles/PGS018642.txt.gz
PGS018643
(TPMI_228_PRS-CS)
 PGP000835 |
Chen HH et al. Nature (2025)
 Hemangioma and lymphangioma any site lymphangioma,
hemangioma		 983,831
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018643/ScoringFiles/PGS018643.txt.gz
PGS018644
(TPMI_228_SBayesR)
 PGP000835 |
Chen HH et al. Nature (2025)
 Hemangioma and lymphangioma any site lymphangioma,
hemangioma		 1,011,189
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS018644/ScoringFiles/PGS018644.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
PPM036822 PGS018640
(TPMI_228_Lassosum2)
 PSS012543|
East Asian Ancestry|
19,931 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Hemangioma and lymphangioma any site — AUROC: 0.69821 R²: 0.01403 sex, age, array, PCs 1-10 —
PPM036823 PGS018641
(TPMI_228_LDpred2)
 PSS012542|
East Asian Ancestry|
19,931 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Hemangioma and lymphangioma any site — AUROC: 0.69822 R²: 0.01417 sex, age, array, PCs 1-10 —
PPM036824 PGS018642
(TPMI_228_MegaPRS)
 PSS012544|
East Asian Ancestry|
19,931 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Hemangioma and lymphangioma any site — AUROC: 0.69622 R²: 0.0139 sex, age, array, PCs 1-10 —
PPM036825 PGS018643
(TPMI_228_PRS-CS)
 PSS012545|
East Asian Ancestry|
19,931 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Hemangioma and lymphangioma any site — AUROC: 0.69929 R²: 0.01429 sex, age, array, PCs 1-10 —
PPM036826 PGS018644
(TPMI_228_SBayesR)
 PSS012546|
East Asian Ancestry|
19,931 individuals
 PGP000835 |
Chen HH et al. Nature (2025)
 Reported Trait: Hemangioma and lymphangioma any site — AUROC: 0.69698 R²: 0.01388 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
PSS012542 228,D18 —
[
  • 185 cases
  • , 19,746 controls
]
,
46.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012543 228,D18 —
[
  • 185 cases
  • , 19,746 controls
]
,
46.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012544 228,D18 —
[
  • 185 cases
  • , 19,746 controls
]
,
46.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012545 228,D18 —
[
  • 185 cases
  • , 19,746 controls
]
,
46.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —
PSS012546 228,D18 —
[
  • 185 cases
  • , 19,746 controls
]
,
46.0 % Male samples
 — East Asian
(Han Chinese)		 — TPMI —