Is CFAP95 p.Arg80Gln (c.239G>A) pathogenic?

CFAP95 p.Arg80Gln (c.239G>A) is classified Uncertain significance in CFAP95 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-02). AlphaMissense: likely benign (0.1568); Rare (popmax 0.106%, nfe).

How common is CFAP95 p.Arg80Gln (c.239G>A) in the general population?

CFAP95 p.Arg80Gln (c.239G>A) is rare (popmax 0.106%, nfe) (gnomAD).

What do computational predictors say about CFAP95 p.Arg80Gln (c.239G>A)?

AlphaMissense predicts likely benign (score 0.1568) — an in-silico prediction, not a clinical call.

CFAP95 p.Arg80Gln

c.239G>A · rs147780802 · VCV3143743

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1568 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.106%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1568	likely benign
REVEL	0.222	benign-leaning
SaProt	LLR -7.24	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 7.2	GERP 1.6, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 85 kb · p 0.17 · regional, not allelic
Overall
CADD	24.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.106% European (non-Finnish) · 1,248/1,179,136 alleles

Filtering AF 0.101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.099%

Overall 0.082% 1,322/1,612,516 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.106%	945
Remaining individualsnot grpmax-eligible	0.0432%	2,312
Finnishnot grpmax-eligible	0.0328%	3,048
African / African-American	0.024%	4,163
Admixed American	0.00836%	11,956
South Asian	0.0033%	30,289

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: CFAP95
Protein: p.Arg80Gln
Coding: c.239G>A
MANE Select: NM_001010940
dbSNP: rs147780802
Type: single nucleotide variant
Location: chr9:69844603 (GRCh38)
Structure: AlphaFold pLDDT 63.03 · 2 PDB

Full CFAP95 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP95 c.381-6T>C Benign ★★ same type
CFAP95 p.Ser122= Benign ★★ same type
CFAP95 p.His169Arg Uncertain significance ★ ⚠ same type
CFAP95 p.Tyr156Cys Uncertain significance ★ ⚠ same type
CFAP95 p.Ser157= Likely benign ★ 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/cfap95-p-arg80gln (accessed [today's date]).

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