Benign chondrogenic neoplasm

Summary

Benign chondrogenic neoplasm (MONDO:0024470) is a cancer with 10 GWAS associations across 5 studies. A subtype of benign neoplasm — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Classification: Cancer
• GWAS associations: 10

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	benign chondrogenic neoplasm
Mondo ID	MONDO:0024470
NCIT	C8592
SNOMED CT	722690001
UMLS	C0852519
MedGen	208867
Is cancer (heuristic)	yes

Also known as: benign cartilaginous neoplasm · benign cartilaginous tumor · benign cartilaginous tumour · benign chondrogenic neoplasm · benign chondrogenic tumor · benign chondrogenic tumour · benign neoplasm of cartilage · benign neoplasm of the cartilage · benign tumor of cartilage · benign tumor of the cartilage · benign tumour of cartilage · benign tumour of the cartilage · chondrogenic neoplasm, benign

Data availability: 10 GWAS associations (5 studies).

Disease family

This is a subtype of benign 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 etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › benign neoplasm › benign chondrogenic neoplasm

Related subtypes (28): respiratory system benign neoplasm, benign reproductive system neoplasm, benign digestive system neoplasm, benign endocrine neoplasm, cardiovascular organ benign neoplasm, immune system organ benign neoplasm, thoracic benign neoplasm, musculoskeletal system benign neoplasm, nervous system benign neoplasm, peritoneal benign neoplasm, integumentary system benign neoplasm, benign mesothelioma, benign mesenchymoma, benign perivascular tumor, benign urinary system neoplasm, calcifying fibrous tumor, pheochromocytoma, benign mastocytoma, benign neoplasm of oral cavity, benign neoplasm of neck, benign neoplasm of salivary gland, benign neoplasm of lip, benign neoplasm of floor of mouth, benign neoplasm of pharynx, benign neoplasm of buccal mucosa, benign epithelial neoplasm, benign phyllodes tumor, germ cell benign neoplasm

Subtypes (3): chondroma, chondroblastoma, chondromyxoid fibroma

Genetics & variants

GWAS landscape

10 GWAS associations across 5 studies. Top hits map to 7 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs145011008	1e-13	RBM45	T	3.34
rs118137644	2e-13	MSANTD2P1 - RNU2-55P	G	2.76
rs185990766	1e-12	ARRDC3-AS1	C	4.39
rs190979921	7e-12	LINC01470	C	3.47
rs565301439	7e-12	KNOP1P1 - RN7SL38P	C	2.95
rs138162229	8e-12	ARHGAP20	G	3.19
rs182407566	9e-12	SIPA1L2	G	2.85
rs753281643	2e-11	GRXCR2	A	3.14
rs185288821	2e-11	NFKBIL1 - LTA	C	2.99
rs188442131	1e-08	GNG4	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90477258	Verma A	2024	717	448,500	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90435659	Zhou W	2018	320	371,171	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90479839	Verma A	2024	268	120,957	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90481553	Verma A	2024	268	120,957	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651504	Liu TY	2025	203	188,123	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	1
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	9

MAF distribution

Bucket	Variants
common (>=0.05)	0
low_freq (0.01-0.05)	0
rare (<0.01)	9
unknown	1

Functional consequences

Consequence	Count
intron_variant	8
missense_variant	1
intergenic_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs145011008	2	178126053	T>A,C	0.001	missense_variant	RBM45	1e-13	Tier 1: coding
rs118137644	21	23158602	G>A,T	0.001	intergenic_variant	MSANTD2P1 - RNU2-55P	2e-13	Tier 4: intronic/intergenic
rs185990766	5	91669777	C>T	0	intron_variant	ARRDC3-AS1	1e-12	Tier 4: intronic/intergenic
rs190979921	5	153216320	C>A,T	0.002	intron_variant	LINC01470	7e-12	Tier 4: intronic/intergenic
rs565301439	12	24667575	C>A	0	intron_variant	KNOP1P1 - RN7SL38P	7e-12	Tier 4: intronic/intergenic
rs138162229	11	110592370	G>T	0.001	intron_variant	ARHGAP20	8e-12	Tier 4: intronic/intergenic
rs182407566	1	232552219	G>A,C	0	intron_variant	SIPA1L2	9e-12	Tier 4: intronic/intergenic
rs753281643	5	145863562	A>C	0.001	intron_variant	GRXCR2	2e-11	Tier 4: intronic/intergenic
rs185288821	6	31564515	C>T	0	intron_variant	NFKBIL1 - LTA	2e-11	Tier 4: intronic/intergenic
rs188442131	1	235576168	C>G		intron_variant	GNG4	1e-08	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.