Is ACP2 p.Ser94= (c.282T>G) pathogenic?

ACP2 p.Ser94= (c.282T>G) is classified Benign in ACP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-20). Rare (popmax 0.241%, eas).

How common is ACP2 p.Ser94= (c.282T>G) in the general population?

ACP2 p.Ser94= (c.282T>G) is rare (popmax 0.241%, eas) (gnomAD).

ACP2 p.Ser94=

c.282T>G · rs372895853 · VCV788072

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.241%, eas)

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 0.31	GERP -3.7, phastCons 0.51
Overall
CADD	8.835	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.241% East Asian · 108/44,886 alleles

Filtering AF 0.204% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.19%

Overall 0.015% 242/1,614,186 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.241%	416
Remaining individualsnot grpmax-eligible	0.192%	521
Admixed American	0.0117%	8,573
African / African-American	0.00533%	18,765
European (non-Finnish)	0.000254%	393,343

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: ACP2
Protein: p.Ser94=
Coding: c.282T>G
MANE Select: NM_001610
dbSNP: rs372895853
Type: single nucleotide variant
Location: chr11:47247656 (GRCh38)
Gene constraint: LOEUF 0.804 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.09

Full ACP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACP2 c.856-4G>A Benign ★★ same type
ACP2 p.Arg10Trp Likely benign ★★ same type
ACP2 p.Phe393Leu Benign/Likely benign ★★ same type
ACP2 p.Val416= Benign ★★ same type
ACP2 p.Ala11Glu Uncertain significance ★ ⚠ same type
ACP2 p.Ala272Val Uncertain significance ★ ⚠ same type
ACP2 p.Ala336Thr Uncertain significance ★ ⚠ same type
ACP2 p.Ala336Val 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/acp2-p-ser94 (accessed [today's date]).

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