Is EBAG9 p.Arg28= (c.84A>G) pathogenic?

EBAG9 p.Arg28= (c.84A>G) is classified Likely benign in EBAG9 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-09). Very rare (popmax 0.00538%, afr).

How common is EBAG9 p.Arg28= (c.84A>G) in the general population?

EBAG9 p.Arg28= (c.84A>G) is very rare (popmax 0.00538%, afr) (gnomAD).

EBAG9 p.Arg28=

c.84A>G · VCV3506350

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00538%, 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 1.6	GERP -2.5, phastCons 1
Overall
CADD	12.41	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00538% African / African-American · 4/74,400 alleles

Filtering AF 0.00176% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.000436% 7/1,604,998 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00538%	18,600
European (non-Finnish)	0.000255%	392,451

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: EBAG9
Protein: p.Arg28=
Coding: c.84A>G
MANE Select: NM_004215
Type: single nucleotide variant
Location: chr8:109553865 (GRCh38)
Gene constraint: LOEUF 0.664 · pLI 0.65 (gnomAD)
Structure: AlphaFold pLDDT 66.63

Full EBAG9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EBAG9 p.Arg28Gly Uncertain significance ★ ⚠ same residue
EBAG9 c.162+5G>T Benign ★★ same type
EBAG9 p.Ala2Thr Uncertain significance ★ ⚠ same type
EBAG9 p.Arg199Gln Uncertain significance ★ ⚠ same type
EBAG9 p.Arg33Trp Uncertain significance ★ ⚠ same type
EBAG9 p.Arg7Gln Uncertain significance ★ ⚠ same type
EBAG9 p.Asp122Glu Uncertain significance ★ ⚠ same type
EBAG9 p.Asp136Tyr 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/ebag9-p-arg28 (accessed [today's date]).

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