Benign digestive system neoplasm

Summary

Benign digestive system neoplasm (MONDO:0000385) is a cancer (an umbrella term covering 10 Mondo subtypes) with 2 GWAS associations across 6 studies. A subtype of digestive system disorder — 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: 2

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	benign digestive system neoplasm
Mondo ID	MONDO:0000385
DOID	DOID:0050624
NCIT	C4787
UMLS	C0497538
MedGen	141680
Anatomy (UBERON)	UBERON:0005409
Is cancer (heuristic)	yes

Also known as: alimentary part of gastrointestinal system benign neoplasm · benign digestive system tumor · benign digestive system tumour · benign gastrointestinal neoplasm · benign gastrointestinal system tumor · benign gastrointestinal system tumour · benign gastrointestinal tumor · benign gastrointestinal tumour · benign GI neoplasm · benign GI system neoplasm · benign GI system tumor · benign GI system tumour · benign GI tumor · benign GI tumour · benign neoplasm of digestive system · benign neoplasm of gastrointestinal system · benign neoplasm of the digestive system · benign tumor of digestive system · benign tumor of gastrointestinal system · benign tumor of GI system (+9 more)

Data availability: 2 GWAS associations (6 studies).

Disease family

This is a subtype of digestive system disorder. 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 › digestive system disorder › benign digestive system neoplasm

Related subtypes (30): autoimmune disorder of gastrointestinal tract, gastrointestinal mucositis, diarrheal disease, pancreas disorder, hepatobiliary disorder, digestive system cancer, peptic ulcer disease, stomach disorder, intestinal disorder, Meckel diverticulum, Cronkhite-Canada syndrome, diverticulosis, small-intestinal, diverticulosis of bowel, hernia, and retinal detachment, congenital enteropathy due to enteropeptidase deficiency, hereditary mixed polyposis syndrome, caudal duplication, Moyamoya disease with early-onset achalasia, hyperplastic polyposis syndrome, thoraco-abdominal enteric duplication, digestive duplication, juvenile polyposis syndrome, umbilical cord ulceration-intestinal atresia syndrome, growth retardation-mild developmental delay-chronic hepatitis syndrome, common mesentery, neoplasm of oropharynx, gastrointestinal polyp, digestive system neuroendocrine neoplasm, digestive system infectious disorder, upper digestive tract disorder, congenital peritoneal encapsulation

Subtypes (10): intestinal benign neoplasm, bile duct papillary neoplasm, pleomorphic adenoma, hepatocellular adenoma, benign neoplasm of stomach, benign neoplasm of esophagus, benign neoplasm of pancreas, benign neoplasm of oropharynx, benign neoplasm of gallbladder, hepatobiliary benign neoplasm

Genetics & variants

GWAS landscape

2 GWAS associations across 6 studies. Top hits map to 1 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs137954472	3e-11	RN7SKP48 - ARHGAP24	A	1.34
rs7599768	3e-07	LPIN1	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90435657	Zhou W	2018	5,280	395,301	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90652065	Liu TY	2025	4,664	216,363	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90477256	Verma A	2024	3,695	438,189	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90477255	Verma A	2024	980	118,773	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479838	Verma A	2024	980	118,773	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90481551	Verma A	2024	407	58,440	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	2

MAF distribution

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

Functional consequences

Consequence	Count
intergenic_variant	1
intron_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs137954472	4	85115826	A>G	0.004	intergenic_variant	RN7SKP48 - ARHGAP24	3e-11	Tier 4: intronic/intergenic
rs7599768	2	11730179	C>T	0.05	intron_variant	LPIN1	3e-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.