Is CFAP92 p.Asp68Asn (c.202G>A) pathogenic?

CFAP92 p.Asp68Asn (c.202G>A) is classified Uncertain significance in CFAP92 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-27). AlphaMissense: likely benign (0.215); Ultra-rare (popmax 0.04%, afr).

How common is CFAP92 p.Asp68Asn (c.202G>A) in the general population?

CFAP92 p.Asp68Asn (c.202G>A) is ultra-rare (popmax 0.04%, afr) (gnomAD).

What do computational predictors say about CFAP92 p.Asp68Asn (c.202G>A)?

AlphaMissense predicts likely benign (score 0.215) — an in-silico prediction, not a clinical call.

CFAP92 p.Asp68Asn

c.202G>A · VCV4227230

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.215 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.04%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.215	likely benign
REVEL	0.072	moderately benign-leaning
SaProt	LLR -7.33	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 2.8	GERP 1.7, phastCons 0.98
Regional constraint	o/e 0.94	unconstrained · MANE · 83 kb · p 0.026 · regional, not allelic
Overall
CADD	21.8	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 0.04% African / African-American · 30/75,070 alleles

Filtering AF 0.0288% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0249%

Overall 0.00279% 45/1,614,090 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.04%	2,502
Admixed American	0.0133%	7,504
Ashkenazi Jewishnot grpmax-eligible	0.0101%	9,869
Remaining individualsnot grpmax-eligible	0.0032%	31,245
South Asian	0.0011%	91,090
European (non-Finnish)	8.48e-05%	1,179,915

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: CFAP92
Protein: p.Asp68Asn
Coding: c.202G>A
MANE Select: NM_001394090
Type: single nucleotide variant
Location: chr3:128993103 (GRCh38)
Gene constraint: LOEUF 0.959 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 57.39

Full CFAP92 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACAD9 c.1692+1G>A Likely pathogenic ★★ same type
ACAD9 p.Arg532Gln Likely pathogenic ★★ ⚠ same type
ACAD9 p.Asn569His Uncertain significance ★★ ⚠ same type
ACAD9 p.Glu596Lys Uncertain significance ★★ ⚠ same type
ACAD9 c.1692+145G>C Benign ★★ same type
ACAD9 c.*26C>T Benign/Likely benign ★★ same type
ACAD9 c.*331T>G Benign/Likely benign ★★ same type
ACAD9 c.*68C>T 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/cfap92-p-asp68asn (accessed [today's date]).

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