Benign soft tissue neoplasm

Summary

Benign soft tissue neoplasm (MONDO:0044335) is a cancer (an umbrella term covering 10 Mondo subtypes) with 4 GWAS associations across 6 studies. A subtype of benign connective and soft tissue neoplasm — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Classification: Cancer
• Umbrella term: 10 Mondo subtypes
• GWAS associations: 4

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	benign soft tissue neoplasm
Mondo ID	MONDO:0044335
NCIT	C4242
SNOMED CT	92069005
UMLS	C0334450
MedGen	83151
Is cancer (heuristic)	yes

Also known as: benign neoplasm of soft tissue · benign neoplasm of the soft tissue · benign soft tissue neoplasm · benign soft tissue tumor · benign soft tissue tumour · benign tumor of soft tissue · benign tumor of the soft tissue · benign tumour of soft tissue · benign tumour of the soft tissue · soft tissue neoplasm, benign

Data availability: 4 GWAS associations (6 studies).

Disease family

This is a subtype of benign connective and soft tissue neoplasm. Genetic, therapeutic, and trial evidence is largely curated at the broader-term level — see the parent page for the associated-gene cohort and molecular evidence.

Classification path: disease › human disease › disease by body system or component › musculoskeletal system disorder › musculoskeletal system benign neoplasm › benign connective and soft tissue neoplasm › benign soft tissue neoplasm

Related subtypes (4): bone benign neoplasm, benign lipomatous neoplasm, benign osteogenic neoplasm, lipofibromatosis

Subtypes (10): endobronchial lipoma, endometrial stromal nodule, fibroosseous pseudotumor of the digits, angiomyxoma, soft tissue chondroma, lipoblastoma, infantile myofibromatosis, benign PEComa, benign synovial neoplasm, myxoma

Genetics & variants

GWAS landscape

4 GWAS associations across 6 studies. Top hits map to 3 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs187100997	2e-12	EPHB1	C	1.39
rs77027504	1e-11	RPL6P5 - METAP2P1	G	2.07
rs188258543	1e-11	MIR4300HG	T	2.21
rs140414549	1e-07	ERBB4	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90477264	Verma A	2024	2,321	442,008	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651904	Liu TY	2025	1,782	233,102	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90435662	Zhou W	2018	1,110	401,613	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90477263	Verma A	2024	963	119,013	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479842	Verma A	2024	963	119,013	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90481554	Verma A	2024	296	58,878	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	0
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	4

MAF distribution

Bucket	Variants
common (>=0.05)	0
low_freq (0.01-0.05)	0
rare (<0.01)	3
unknown	1

Functional consequences

Consequence	Count
intron_variant	3
intergenic_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs187100997	3	134837362	C>T	0.002	intron_variant	EPHB1	2e-12	Tier 4: intronic/intergenic
rs77027504	2	145463896	G>A	0.002	intergenic_variant	RPL6P5 - METAP2P1	1e-11	Tier 4: intronic/intergenic
rs188258543	11	82448156	T>G	0	intron_variant	MIR4300HG	1e-11	Tier 4: intronic/intergenic
rs140414549	2	211925584	T>C		intron_variant	ERBB4	1e-07	Tier 4: intronic/intergenic

Genes & proteins

No associated-gene cohort resolved for this disease. Atlas builds the molecular and therapeutic sections — associated genes, protein families, druggability, pathways, interactions, and drug associations — by aggregating over a disease’s associated genes (resolved via GWAS / GenCC / ClinVar / CIViC), and none resolved here. This is expected for antibody-mediated, autoimmune, or otherwise non-gene-defined conditions; the curated evidence for this disease is its clinical features, GWAS susceptibility, and clinical trials (above).

Function

No pathway enrichment — requires an associated-gene cohort.

Therapeutics

No druggable-target or therapeutic data for this disease’s cohort.

Clinical trials & evidence

Clinical trials

Clinical trials: 0.