Benign thyroid gland neoplasm

Summary

Benign thyroid gland neoplasm (MONDO:0006107) is a cancer with 10 GWAS associations across 6 studies and 5 clinical trials. A subtype of benign endocrine 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 trials: 5

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	benign thyroid gland neoplasm
Mondo ID	MONDO:0006107
EFO	EFO:1000122
ICD-10-CM	D34
NCIT	C3628
SNOMED CT	92439006
UMLS	C0154038
MedGen	102306
GARD	0024295
Anatomy (UBERON)	UBERON:0002046
Is cancer (heuristic)	yes

Also known as: benign neoplasm of the thyroid · benign neoplasm of the thyroid gland · benign neoplasm of thyroid · benign neoplasm of thyroid gland · benign neoplasm of thyroid glands · benign thyroid gland neoplasm · benign thyroid gland tumor · benign thyroid gland tumour · benign thyroid neoplasm · benign thyroid tumor · benign thyroid tumour · benign tumor of the thyroid · benign tumor of the thyroid gland · benign tumor of thyroid · benign tumor of thyroid gland · benign tumour of the thyroid · benign tumour of the thyroid gland · benign tumour of thyroid · benign tumour of thyroid gland · thyroid gland benign neoplasm (+1 more)

Data availability: 10 GWAS associations (6 studies).

Disease family

This is a subtype of benign endocrine 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 › endocrine gland neoplasm › benign endocrine neoplasm › benign thyroid gland neoplasm

Related subtypes (13): liver lipoma, liver hemangioma, bile duct papillary neoplasm, liver leiomyoma, benign carotid body paraganglioma, pineocytoma, hepatocellular adenoma, benign neoplasm of pituitary gland, benign neoplasm of parathyroid gland, benign neoplasm of adrenal gland, benign neoplasm of thymus, TMEM127-related tumor predisposition, MAX-related tumor predisposition

Subtypes (1): follicular thyroid adenoma

Genetics & variants

GWAS landscape

10 GWAS associations across 6 studies. Top hits map to 9 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs72811672	2e-12	ADAP2 - LINC02978	T	2.01
rs73252941	3e-12	PDGFRA	C	2.17
rs573372786	6e-12	NPAS2	C	3.41
rs193101356	6e-12	C4orf50, JAKMIP1	G	2.59
rs117913733	7e-12	CD7 - SECTM1	?
rs567136875	8e-12	RGL1	C	3.81
rs571860225	1e-11	LRCH1	G	2.93
rs558445452	2e-11	PALM2AKAP2	G	2.55
rs185328616	3e-11	PPP1R12B, SYT2	C	3.37
rs564462645	3e-11	RHOH - LINC02265	G	3.75

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90477287	Verma A	2024	764	449,292	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90435677	Zhou W	2018	285	407,399	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90479853	Verma A	2024	281	121,213	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90481559	Verma A	2024	281	121,213	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90043608	Jiang L	2021	267	456,081	A generalized linear mixed model association tool for biobank-scale data.
GCST90651229	Liu TY	2025	179	234,488	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	0
Tier 2: splice/UTR	1
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	6
intergenic_variant	3
3_prime_UTR_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs72811672	17	30960654	T>A,C	0.002	intergenic_variant	ADAP2 - LINC02978	2e-12	Tier 4: intronic/intergenic
rs73252941	4	54231424	C>T	0.001	intron_variant	PDGFRA	3e-12	Tier 4: intronic/intergenic
rs573372786	2	100821896	C>T	0	intron_variant	NPAS2	6e-12	Tier 4: intronic/intergenic
rs193101356	4	6028771	G>A	0	intron_variant	C4orf50, JAKMIP1	6e-12	Tier 4: intronic/intergenic
rs117913733	17	82319571	G>A		intergenic_variant	CD7 - SECTM1	7e-12	Tier 4: intronic/intergenic
rs567136875	1	183797496	C>T	0.001	intron_variant	RGL1	8e-12	Tier 4: intronic/intergenic
rs571860225	13	46613567	G>A	0.001	intron_variant	LRCH1	1e-11	Tier 4: intronic/intergenic
rs558445452	9	110127922	G>A	0.001	intron_variant	PALM2AKAP2	2e-11	Tier 4: intronic/intergenic
rs185328616	1	202592458	C>T	0.001	3_prime_UTR_variant	PPP1R12B, SYT2	3e-11	Tier 2: splice/UTR
rs564462645	4	40273459	G>A,C,T	0	intergenic_variant	RHOH - LINC02265	3e-11	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: 5.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	5

Top trials by phase / activity

NCT	Phase	Status	Title
NCT01690806	Not specified	COMPLETED	Dexamethasone for the Prevention of Recurrent Laryngeal Nerve Palsy
NCT01776385	Not specified	COMPLETED	The ISET (Isolation by Size of Epithelial Tumor Cells) and the CellSearch Methods in Malignant Pleural Mesothelioma
NCT04051099	Not specified	UNKNOWN	Bilateral Superficial Cervical Plexus Block in Thyroid/Parathyroid Surgery
NCT04594720	Not specified	COMPLETED	Circulating Biomarkers to Identify Thyroid Cancer
NCT05003856	Not specified	TERMINATED	Radiofrequency Ablation for the Treatment of Benign or Low Risk Thyroid Nodule

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
CHEMBL443232	0	1