Nervous system benign neoplasm
diseaseOn this page
Also known as benign neoplasm of nervous systembenign neoplasm of the nervous systembenign nervous system neoplasmbenign nervous system tumorbenign nervous system tumourbenign tumor of nervous systembenign tumor of the nervous systembenign tumour of nervous systembenign tumour of the nervous systemnervous system neoplasm, benign
Summary
Nervous system benign neoplasm (MONDO:0000648) is a cancer (an umbrella term covering 5 Mondo subtypes) with 10 GWAS associations across 13 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
- Umbrella term: 5 Mondo subtypes
- GWAS associations: 10
Clinical features
No curated clinical features (Orphanet) for this disease.
Identifiers
Disease identifiers
| Field | Value |
|---|---|
| Canonical name | nervous system benign neoplasm |
| Mondo ID | MONDO:0000648 |
| DOID | DOID:0060115 |
| NCIT | C4789 |
| SNOMED CT | 92247009 |
| UMLS | C0497550 |
| MedGen | 99232 |
| Anatomy (UBERON) | UBERON:0001016 |
| Is cancer (heuristic) | yes |
Also known as: 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
Data availability: 10 GWAS associations (13 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 › nervous system benign 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, 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 chondrogenic neoplasm, benign epithelial neoplasm, benign phyllodes tumor, germ cell benign neoplasm
Subtypes (5): central nervous system organ benign neoplasm, sensory organ benign neoplasm, neurocutaneous melanocytosis, hemangioblastoma, phakomatosis pigmentokeratotica
Genetics & variants
GWAS landscape
10 GWAS associations across 13 studies. Top hits map to 2 distinct genes (as reported by GWAS).
Top associations by p-value
| rsID | p-value | Gene | Risk allele | Odds ratio |
|---|---|---|---|---|
| rs151125896 | 1e-12 | Y_RNA - SMLR1 | A | 2.54 |
| rs373616995 | 5e-12 | BATF | C | 3.9 |
| rs371637752 | 1e-11 | BATF | T | 3.85 |
| rs117737455 | 2e-11 | GS1-279B7.1 - RNU7-183P | C | 4.14 |
| rs537798415 | 3e-11 | RNA5SP472 - ZNF507 | G | 2.17 |
| rs78378222 | 4e-11 | TP53 | T | 0.61 |
| rs140911425 | 3e-07 | SAMSN1 - POLR2CP1 | ? | |
| rs28707380 | 4e-07 | ELMO2P1 - GOLGA6L1 | ? |
Top studies (by case count)
| Study | Lead author | Year | Cases | Controls | Title |
|---|---|---|---|---|---|
| GCST90477284 | Verma A | 2024 | 2,880 | 446,779 | Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. |
| GCST90477286 | Verma A | 2024 | 2,716 | 447,107 | Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. |
| GCST90652056 | Liu TY | 2025 | 1,229 | 234,636 | Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population. |
| GCST90652101 | Liu TY | 2025 | 1,079 | 234,636 | Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population. |
| GCST90435674 | Zhou W | 2018 | 828 | 407,239 | Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies. |
| GCST90435675 | Zhou W | 2018 | 774 | 407,239 | Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies. |
| GCST90042884 | Jiang L | 2021 | 709 | 455,639 | A generalized linear mixed model association tool for biobank-scale data. |
| GCST90477283 | Verma A | 2024 | 656 | 120,855 | Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. |
| GCST90479852 | Verma A | 2024 | 656 | 120,855 | Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. |
| GCST90477285 | Verma A | 2024 | 613 | 120,931 | 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 | 1 |
| Tier 3: regulatory | 0 |
| Tier 4: intronic/intergenic | 7 |
MAF distribution
| Bucket | Variants |
|---|---|
| common (>=0.05) | 1 |
| low_freq (0.01-0.05) | 0 |
| rare (<0.01) | 6 |
| unknown | 1 |
Functional consequences
| Consequence | Count |
|---|---|
| intron_variant | 4 |
| intergenic_variant | 3 |
| 3_prime_UTR_variant | 1 |
Top variants
| rsID | Chr | Pos | Alleles | MAF | Consequence | Gene | p-value | Tier |
|---|---|---|---|---|---|---|---|---|
| rs151125896 | 6 | 130645272 | A>G,T | 0.001 | intergenic_variant | Y_RNA - SMLR1 | 1e-12 | Tier 4: intronic/intergenic |
| rs373616995 | 14 | 75532870 | C>T | 0 | intron_variant | BATF | 5e-12 | Tier 4: intronic/intergenic |
| rs371637752 | 14 | 75544211 | T>C | 0 | intron_variant | BATF | 1e-11 | Tier 4: intronic/intergenic |
| rs117737455 | 1 | 185412161 | C>T | 0 | intergenic_variant | GS1-279B7.1 - RNU7-183P | 2e-11 | Tier 4: intronic/intergenic |
| rs537798415 | 19 | 32323448 | G>A | 0.001 | intergenic_variant | RNA5SP472 - ZNF507 | 3e-11 | Tier 4: intronic/intergenic |
| rs78378222 | 17 | 7668434 | T>A,G | 0.009 | 3_prime_UTR_variant | TP53 | 4e-11 | Tier 2: splice/UTR |
| rs140911425 | 21 | 14746231 | A>T | intron_variant | SAMSN1 - POLR2CP1 | 3e-07 | Tier 4: intronic/intergenic | |
| rs28707380 | 15 | 23113538 | G>C,T | 0.05 | intron_variant | ELMO2P1 - GOLGA6L1 | 4e-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.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.