Is AGMO p.Thr202= (c.606A>G) pathogenic?

AGMO p.Thr202= (c.606A>G) is classified Benign in AGMO (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-11-27). Common (popmax 13.3%, afr) — too common for a highly-penetrant pathogenic allele.

AGMO p.Thr202=

Q: How common is AGMO p.Thr202= (c.606A>G) in the general population?

AGMO p.Thr202= (c.606A>G) is common (popmax 13.3%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.606A>G · rs28635514 · VCV1236929

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 13.3%, afr) — too common for a highly-penetrant pathogenic allele

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.038	GERP -2.6, phastCons 0.94
Overall
CADD	6.546	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 13.3% African / African-American · 9,650/72,540 alleles

Filtering AF 13.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 13%

Overall 4% 63,240/1,581,894 alleles · common exomes 52,686/1,430,014 · genomes 10,554/151,880 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	13.3%	8
Ashkenazi Jewishnot grpmax-eligible	9.79%	10
Finnishnot grpmax-eligible	7.57%	13
Admixed American	6.55%	15
Middle Eastern	5.84%	17
Remaining individualsnot grpmax-eligible	4.61%	22
Amishnot grpmax-eligible	4.4%	23
European (non-Finnish)	3.19%	31
South Asian	2.35%	43
East Asian	0.0116%	8,640

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: AGMO
Protein: p.Thr202=
Coding: c.606A>G
MANE Select: NM_001004320
dbSNP: rs28635514
Type: single nucleotide variant
Location: chr7:15418561 (GRCh38)
Gene constraint: LOEUF 1.561 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.90
Residue 202: the fatty acid hydroxylase domain

Full AGMO gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AGMO p.Thr202Ile Uncertain significance ★ ⚠ same residue
AGMO p.Arg133Cys Uncertain significance ★★ ⚠ same type
AGMO p.Arg83Gln Uncertain significance ★★ ⚠ same type
AGMO p.Gly238Cys Uncertain significance ★★ ⚠ same type
AGMO p.Gly322Ser Uncertain significance ★★ ⚠ same type
AGMO p.Ile281Val Uncertain significance ★★ ⚠ same type
AGMO p.Leu213Val Uncertain significance ★★ ⚠ same type
AGMO p.Lys234Arg Uncertain significance ★★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/agmo-p-thr202 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown