Is CFAP69 p.Arg106His (c.317G>A) pathogenic?

CFAP69 p.Arg106His (c.317G>A) is classified Benign in CFAP69 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2018-11-15). AlphaMissense: likely benign (0.0617); Low-frequency (popmax 2.74%, afr).

How common is CFAP69 p.Arg106His (c.317G>A) in the general population?

CFAP69 p.Arg106His (c.317G>A) is low-frequency (popmax 2.74%, afr) (gnomAD).

What do computational predictors say about CFAP69 p.Arg106His (c.317G>A)?

AlphaMissense predicts likely benign (score 0.0617) — an in-silico prediction, not a clinical call.

CFAP69 p.Arg106His

c.317G>A · rs151205971 · VCV712004

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0617 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.74%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.0617	likely benign
SaProt	LLR -6.85	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.2	GERP -8.4
Regional constraint	o/e 0.97	unconstrained · MANE · 65 kb · p 0.37 · regional, not allelic
Overall
CADD	0.726	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 2.74% African / African-American · 2,032/74,278 alleles

Filtering AF 2.64% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.6%

Overall 0.149% 2,382/1,602,988 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.74%	37
Admixed American	0.205%	488
Remaining individualsnot grpmax-eligible	0.198%	505
Middle Eastern	0.0829%	1,206
European (non-Finnish)	0.00834%	11,996
South Asian	0.00452%	22,116
East Asian	0.00225%	44,388

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: CFAP69
Protein: p.Arg106His
Coding: c.317G>A
MANE Select: NM_001039706
dbSNP: rs151205971
Type: single nucleotide variant
Location: chr7:90262017 (GRCh38)
Gene constraint: LOEUF 1 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.48

Full CFAP69 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP69 p.Arg106Ser Uncertain significance ★ ⚠ same residue
CFAP69 p.Phe731Leu Uncertain significance ★★ ⚠ same type
CFAP69 p.Tyr819His Uncertain significance ★★ ⚠ same type
CFAP69 c.1857+47T>A Benign ★★ same type
CFAP69 c.682+50A>C Benign ★★ same type
CFAP69 p.Ala12= Benign ★★ same type
CFAP69 p.Ala182= Benign ★★ same type
CFAP69 p.Ala8= Benign/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/cfap69-p-arg106his (accessed [today's date]).

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