Is CD86 p.Asp323Asn (c.967G>A) pathogenic?

CD86 p.Asp323Asn (c.967G>A) is classified Benign in CD86 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-03-29). AlphaMissense: likely benign (0.0809); Low-frequency (popmax 2.96%, afr).

How common is CD86 p.Asp323Asn (c.967G>A) in the general population?

CD86 p.Asp323Asn (c.967G>A) is low-frequency (popmax 2.96%, afr) (gnomAD).

What do computational predictors say about CD86 p.Asp323Asn (c.967G>A)?

AlphaMissense predicts likely benign (score 0.0809) — an in-silico prediction, not a clinical call.

CD86 p.Asp323Asn

c.967G>A · rs9282648 · VCV720917

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0809 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.96%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0809	likely benign
REVEL	0.042	moderately benign-leaning
SaProt	LLR -6.01	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 -0.48	GERP -3.1
Regional constraint	o/e 0.90	unconstrained · MANE · 64 kb · p 0.048 · regional, not allelic
Overall
CADD	3.995	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 2.96% African / African-American · 2,207/74,678 alleles

Filtering AF 2.85% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.81%

Overall 0.191% 3,051/1,601,248 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.96%	34
Middle Eastern	0.415%	241
Admixed American	0.34%	294
Remaining individualsnot grpmax-eligible	0.271%	369
European (non-Finnish)	0.0378%	2,644
South Asian	0.00441%	22,681
East Asian	0.00223%	44,796

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: CD86
Protein: p.Asp323Asn
Coding: c.967G>A
MANE Select: NM_175862
dbSNP: rs9282648
Type: single nucleotide variant
Location: chr3:122119511 (GRCh38)
Gene constraint: LOEUF 0.555 · pLI 0.93 (gnomAD)
Structure: AlphaFold pLDDT 80.10 · 7 PDB
Residue 323: a UniProt-annotated variant site (in); the 'disordered' region

Full CD86 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD86 p.Ala310Thr Benign ★★ same type
CD86 p.Ala24Val Uncertain significance ★ ⚠ same type
CD86 p.Arg277Cys Uncertain significance ★ ⚠ same type
CD86 p.Arg277His Uncertain significance ★ ⚠ same type
CD86 p.Arg306Ile Uncertain significance ★ ⚠ same type
CD86 p.Asp104Glu Uncertain significance ★ ⚠ same type
CD86 p.Gln311Glu Uncertain significance ★ ⚠ same type
CD86 p.Glu181Ala 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/cd86-p-asp323asn (accessed [today's date]).

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