Benign neoplasm of skin

Summary

Benign neoplasm of skin (MONDO:0021440) is a cancer (an umbrella term covering 12 Mondo subtypes) with 18 GWAS associations across 20 studies and 3 clinical trials. A subtype of integumentary system benign neoplasm — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Classification: Cancer
• Umbrella term: 12 Mondo subtypes
• GWAS associations: 18
• Clinical trials: 3

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	benign neoplasm of skin
Mondo ID	MONDO:0021440
NCIT	C2896
SNOMED CT	92384009
UMLS	C0004998
MedGen	2197
Anatomy (UBERON)	UBERON:0000014
Is cancer (heuristic)	yes

Also known as: benign cutaneous neoplasm · benign cutaneous tumor · benign cutaneous tumour · benign neoplasm of the skin · benign skin neoplasm · benign skin tumor · benign skin tumour · benign tumor of skin · benign tumor of the skin · benign tumour of skin · benign tumour of the skin · skin neoplasms, benign · zone of skin benign neoplasm

Data availability: 18 GWAS associations (20 studies).

Disease family

An umbrella term covering 12 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › integumentary system disorder › integumentary system benign neoplasm › benign neoplasm of skin

Related subtypes (7): Bartholin gland benign neoplasm, hemangioma of subcutaneous tissue, adiposis dolorosa, multiple symmetric lipomatosis, familial multiple lipomatosis, intraductal breast papilloma, adenoma of nipple

Subtypes (12): bacillary angiomatosis, skin lipoma, skin hemangioma, leiomyoma cutis, melanocytic nevus, encephalocraniocutaneous lipomatosis, familial multiple fibrofolliculoma, benign neoplasm of sweat gland, benign neoplasm of sebaceous gland, benign eyelid neoplasm, benign epithelial skin neoplasm, skin lymphangioma

Genetics & variants

GWAS landscape

18 GWAS associations across 20 studies. Top hits map to 10 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs112096783	8e-20	CDKN2B-AS1	T	0.31
rs2064103	2e-19	MAFF, PLA2G6	T	0.07
rs4268748	7e-19	DEF8	T	0.07
rs78378222	8e-17	TP53	T	0.26
rs8051733	8e-15	DEF8	A	0.06
chr11:89021574	9e-15		G	0.06
rs16891982	1e-13	SLC45A2	C	0.16
rs111929914	3e-13	ATM	C	0.08
rs7101897	3e-13	TYR	C	0.06
chr2:202151163	1e-12		A	0.06
rs7582362	2e-11	CASP8, FLACC1	A	0.05
chr3:169489103	3e-11		G	0.06
rs141733469	7e-08	LINP1 - LINC02665	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90475620	Verma A	2024	38,768	359,753	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90079683	Backman JD	2021	7,862	369,330	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083669	Backman JD	2021	7,862	369,330	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90435663	Zhou W	2018	7,722	400,618	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90651778	Liu TY	2025	6,382	222,939	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90477266	Verma A	2024	3,834	110,031	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479844	Verma A	2024	3,834	110,031	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90477265	Verma A	2024	2,867	51,872	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90079678	Backman JD	2021	1,342	386,579	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083664	Backman JD	2021	1,342	386,579	Exome sequencing and analysis of 454,787 UK Biobank participants.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	1
Tier 2: splice/UTR	1
Tier 3: regulatory	0
Tier 4: intronic/intergenic	11

MAF distribution

Bucket	Variants
common (>=0.05)	9
low_freq (0.01-0.05)	3
rare (<0.01)	0
unknown	1

Functional consequences

Consequence	Count
intron_variant	8
unknown	3
3_prime_UTR_variant	1
missense_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs112096783	9	22049457	T>C	0.021	intron_variant	CDKN2B-AS1	8e-20	Tier 4: intronic/intergenic
rs2064103	22	38212220	T>A,C	0.457	intron_variant	MAFF, PLA2G6	2e-19	Tier 4: intronic/intergenic
rs4268748	16	89960104	T>C	0.281	intron_variant	DEF8	7e-19	Tier 4: intronic/intergenic
rs78378222	17	7668434	T>A,G	0.012	3_prime_UTR_variant	TP53	8e-17	Tier 2: splice/UTR
rs8051733	16	89957798	A>G	0.314	intron_variant	DEF8	8e-15	Tier 4: intronic/intergenic
chr11:89021574				0.314			9e-15	Tier 4: intronic/intergenic
rs16891982	5	33951588	C>A,G	0.037	missense_variant	SLC45A2	1e-13	Tier 1: coding
rs111929914	11	108275572	C>G,T	0.138	intron_variant	ATM	3e-13	Tier 4: intronic/intergenic
rs7101897	11	89274754	C>T	0.291	intron_variant	TYR	3e-13	Tier 4: intronic/intergenic
chr2:202151163				0.279			1e-12	Tier 4: intronic/intergenic
rs7582362	2	201311571	A>G	0.281	intron_variant	CASP8, FLACC1	2e-11	Tier 4: intronic/intergenic
chr3:169489103				0.246			3e-11	Tier 4: intronic/intergenic
rs141733469	10	7040541	C>G		intron_variant	LINP1 - LINC02665	7e-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: 3.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	3

Top trials by phase / activity

NCT	Phase	Status	Title
NCT06598137	Not specified	ACTIVE_NOT_RECRUITING	Study to Examine Lesions of the Skin Using Confocal Laser Microscopy
NCT06661577	Not specified	NOT_YET_RECRUITING	An Observational Study Using The LumAssure Device In Participants Undergoing Assessment Of Skin Conditions.
NCT04249115	Not specified	TERMINATED	Nano-Pulse Stimulation (NPS) in Seborrheic Keratosis Optimization Study