Is AGMAT p.Ala10= (c.30C>T) pathogenic?

AGMAT p.Ala10= (c.30C>T) is classified Likely benign in AGMAT (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-16). Rare (popmax 0.327%, afr).

How common is AGMAT p.Ala10= (c.30C>T) in the general population?

AGMAT p.Ala10= (c.30C>T) is rare (popmax 0.327%, afr) (gnomAD).

AGMAT p.Ala10=

c.30C>T · rs549635682 · VCV784932

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.327%, afr)

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 0.19	GERP -4.4
Overall
CADD	6.833	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.327% African / African-American · 214/65,422 alleles

Filtering AF 0.291% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.277%

Overall 0.0206% 282/1,366,280 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.327%	306
Admixed American	0.143%	700
Remaining individualsnot grpmax-eligible	0.0483%	2,072
South Asian	0.00177%	56,624
European (non-Finnish)	0.000374%	267,045

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: AGMAT
Protein: p.Ala10=
Coding: c.30C>T
MANE Select: NM_024758
dbSNP: rs549635682
Type: single nucleotide variant
Location: chr1:15584938 (GRCh38)
Gene constraint: LOEUF 1.712 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.12

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

Similar variants

AGMAT p.Ala10Ser Uncertain significance ★ ⚠ same residue
AGMAT p.Thr229Met Benign ★★ same type
AGMAT p.Thr351= Benign ★★ same type
AGMAT p.Ala113Asp Uncertain significance ★ ⚠ same type
AGMAT p.Ala186Val Uncertain significance ★ ⚠ same type
AGMAT p.Ala285Val Uncertain significance ★ ⚠ same type
AGMAT p.Ala335Val Uncertain significance ★ ⚠ same type
AGMAT p.Ala74Ser 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/agmat-p-ala10 (accessed [today's date]).

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