Benign neoplasm
diseaseOn this page
Also known as benign neoplasm (disease)benign tumourbenign unclassifiable tumourneoplasm (disease), benign
Summary
Benign neoplasm (MONDO:0005165) is a cancer (an umbrella term covering 29 Mondo subtypes) with 4 GWAS associations across 39 studies and 14 clinical trials. Top therapeutic interventions include bupivacaine, indocyanine green acid form, and albumin human. A subtype of neoplasm — broader associated-gene and molecular evidence is on the parent page (see Disease family below).
At a glance
- Classification: Cancer
- Umbrella term: 29 Mondo subtypes
- GWAS associations: 4
- Clinical trials: 14
Clinical features
No curated clinical features (Orphanet) for this disease.
Identifiers
Disease identifiers
| Field | Value |
|---|---|
| Canonical name | benign neoplasm |
| Mondo ID | MONDO:0005165 |
| EFO | EFO:0002422 |
| DOID | DOID:0060072, DOID:0060084, DOID:0060085 |
| ICD-10-CM | D10-D36 |
| NCIT | C3677 |
| SNOMED CT | 20376005 |
| UMLS | C0086692 |
| MedGen | 39483 |
| Is cancer (heuristic) | yes |
Also known as: benign neoplasm · benign neoplasm (disease) · benign tumour · benign unclassifiable tumour · neoplasm (disease), benign
Data availability: 4 GWAS associations (39 studies).
Disease family
This is a subtype of 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
Related subtypes (47): pre-malignant neoplasm, endocrine gland neoplasm, giant cell tumor, hematopoietic and lymphoid system neoplasm, skin neoplasm, mesenchymal cell neoplasm, epidural spinal canal neoplasm, skeletal muscle neoplasm, trophoblastic neoplasm, cancer, germ cell tumor, upper aerodigestive tract neoplasm, histiocytoma, embryonal neoplasm, head and neck neoplasm, epithelial neoplasm, reproductive system neoplasm, non-seminomatous lesion, odontogenic cyst, phosphaturic mesenchymal tumor, thyroglossal duct cyst, hamartoma, mesenchymoma, mesothelial neoplasm, peritoneal neoplasm, virus associated tumor, nail tumor, respiratory tract neoplasm, spindle cell neoplasm, mixed neoplasm, urinary system neoplasm, cystic neoplasm, childhood neoplasm, melanocytic neoplasm, digestive system neoplasm, nervous system neoplasm, neoplasm of thorax, connective tissue neoplasm, bronchial adenomas/carcinoids childhood, diffuse idiopathic pulmonary neuroendocrine cell hyperplasia, erythroplakia, retroperitoneal neoplasm, cardiovascular neoplasm, dermoid or epidermoid cyst of the central nervous system, connective and soft tissue neoplasm, NTRK fusion positive cancer, RET fusion positive cancer
Subtypes (29): 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 chondrogenic neoplasm, benign epithelial neoplasm, benign phyllodes tumor, germ cell benign neoplasm
Genetics & variants
GWAS landscape
4 GWAS associations across 39 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 |
|---|---|---|---|---|
| rs538049645 | 2e-11 | RALGPS1, ANGPTL2 | G | 2.88 |
| rs138973941 | 2e-11 | AKIRIN2 - Y_RNA | C | 1.26 |
| rs184305217 | 3e-11 | KCNA5 - LINC02443 | A | 2.4 |
| rs75502905 | 6e-08 | GKN2 | ? |
Top studies (by case count)
| Study | Lead author | Year | Cases | Controls | Title |
|---|---|---|---|---|---|
| GCST90042860 | Jiang L | 2021 | 19,026 | 437,322 | A generalized linear mixed model association tool for biobank-scale data. |
| GCST90477281 | Verma A | 2024 | 4,294 | 405,920 | Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. |
| GCST90477254 | Verma A | 2024 | 3,119 | 442,782 | Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. |
| GCST90042864 | Jiang L | 2021 | 2,863 | 453,485 | A generalized linear mixed model association tool for biobank-scale data. |
| GCST90435683 | Zhou W | 2018 | 2,402 | 406,559 | Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies. |
| GCST90043613 | Jiang L | 2021 | 2,201 | 454,147 | A generalized linear mixed model association tool for biobank-scale data. |
| GCST90079664 | Backman JD | 2021 | 1,532 | 386,164 | Exome sequencing and analysis of 454,787 UK Biobank participants. |
| GCST90083650 | Backman JD | 2021 | 1,532 | 386,164 | Exome sequencing and analysis of 454,787 UK Biobank participants. |
| GCST90044283 | Jiang L | 2021 | 1,425 | 454,923 | A generalized linear mixed model association tool for biobank-scale data. |
| GCST90477280 | Verma A | 2024 | 1,300 | 101,312 | 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 | 4 |
Top variants
| rsID | Chr | Pos | Alleles | MAF | Consequence | Gene | p-value | Tier |
|---|---|---|---|---|---|---|---|---|
| rs538049645 | 9 | 127093435 | G>A,T | 0 | intron_variant | RALGPS1, ANGPTL2 | 2e-11 | Tier 4: intronic/intergenic |
| rs138973941 | 6 | 87822477 | C>G,T | 0.001 | intron_variant | AKIRIN2 - Y_RNA | 2e-11 | Tier 4: intronic/intergenic |
| rs184305217 | 12 | 5218387 | A>C | 0.001 | intron_variant | KCNA5 - LINC02443 | 3e-11 | Tier 4: intronic/intergenic |
| rs75502905 | 2 | 68952837 | A>T | intron_variant | GKN2 | 6e-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: 14.
Phase distribution (across all retrieved trials)
| Phase | Trials |
|---|---|
| Not specified | 10 |
| PHASE4 | 2 |
| PHASE3 | 1 |
| PHASE2 | 1 |
Top trials by phase / activity
| NCT | Phase | Status | Title |
|---|---|---|---|
| NCT05726136 | PHASE4 | RECRUITING | Fluid Challenge and Plasma Volume, During Surgery |
| NCT05082441 | PHASE4 | UNKNOWN | Liposomal Bupivacaine in Benign Soft Tissue Tumor Resection |
| NCT01817075 | PHASE3 | COMPLETED | Chlorhexidine Gluconate Cleansing in Preventing Central Line Associated Bloodstream Infection and Acquisition of Multi-drug Resistant Organisms in Younger Patients With Cancer or Undergoing Donor Stem Cell Transplant |
| NCT04752137 | PHASE2 | RECRUITING | Intraoperative Tumor Margin Identification With ICG Dye Imaging |
| NCT02911064 | Not specified | ACTIVE_NOT_RECRUITING | Expectations Regarding Mobility and Self-Care |
| NCT03626285 | Not specified | AVAILABLE | Bone Marrow Transplantation Using CD34-Selected Stem Cells From Related or Unrelated Donors in Treating Participants With Cancer or Other Disorders |
| NCT00299195 | Not specified | COMPLETED | A Randomized Study of Sulindac in Oral Premalignant Lesions |
| NCT01993199 | Not specified | UNKNOWN | Deep Biopsy Via Endoscopic Submucosal Dissection in Upper GI Subepithelial Tumors |
| NCT02810405 | Not specified | COMPLETED | Collection of Tissue Blocks or Slides From Patients With Cancer |
| NCT03042884 | Not specified | COMPLETED | Wearable Exercise Trackers in Cancer Rehabilitation |
| NCT03429127 | Not specified | UNKNOWN | Normal Saline Vrs Balanced i.v. Fluids in Neurosurgery |
| NCT04360993 | Not specified | COMPLETED | Role of PET/MRI in Head and Neck Cancer |
| NCT05041608 | Not specified | UNKNOWN | Endoscopic Surgery for Gastrointestinal Disorders: A Multicenter Registry Study |
| NCT06174532 | Not specified | UNKNOWN | Virtual Surgical Planning in Mandibular Segmental Resection |
Drugs tested across these trials (top 30)
| Molecule | Max phase | Trials referencing |
|---|---|---|
| BUPIVACAINE | 4 | 2 |
| INDOCYANINE GREEN ACID FORM | 4 | 2 |
| ALBUMIN HUMAN | 4 | 1 |
| SULINDAC | 4 | 1 |