Is AGMO p.Asp9Val (c.26A>T) pathogenic?

AGMO p.Asp9Val (c.26A>T) is classified Benign in AGMO (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). AlphaMissense: likely benign (0.0921); Low-frequency (popmax 4.59%, afr).

How common is AGMO p.Asp9Val (c.26A>T) in the general population?

AGMO p.Asp9Val (c.26A>T) is low-frequency (popmax 4.59%, afr) (gnomAD).

What do computational predictors say about AGMO p.Asp9Val (c.26A>T)?

AlphaMissense predicts likely benign (score 0.0921) — an in-silico prediction, not a clinical call.

AGMO p.Asp9Val

c.26A>T · rs61751889 · VCV787049

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0921 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 4.59%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0921	likely benign
REVEL	0.017	moderately benign-leaning
SaProt	LLR -3.48	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.3	GERP -1.4, phastCons 1
Regional constraint	o/e 1.45	unconstrained · MANE · 361 kb · p 3.8e-25 · regional, not allelic
Overall
CADD	17.78	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.59% African / African-American · 3,435/74,760 alleles

Filtering AF 4.47% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.41%

Overall 0.233% 3,748/1,609,558 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.59%	22
Remaining individualsnot grpmax-eligible	0.236%	424
Admixed American	0.188%	532
Middle Eastern	0.0497%	2,014
European (non-Finnish)	0.00416%	24,027
East Asian	0.00224%	44,698
South Asian	0.0011%	90,512

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.Asp9Val
Coding: c.26A>T
MANE Select: NM_001004320
dbSNP: rs61751889
Type: single nucleotide variant
Location: chr7:15561820 (GRCh38)
Gene constraint: LOEUF 1.561 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.90

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

Similar variants

AGMO p.Asp9Tyr 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-asp9val (accessed [today's date]).

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