Is CFAP96 p.Asp56Val (c.167A>T) pathogenic?

CFAP96 p.Asp56Val (c.167A>T) is classified Uncertain significance in CFAP96 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-06). AlphaMissense: likely benign (0.2195); Very rare (popmax 0.00981%, amr).

How common is CFAP96 p.Asp56Val (c.167A>T) in the general population?

CFAP96 p.Asp56Val (c.167A>T) is very rare (popmax 0.00981%, amr) (gnomAD).

What do computational predictors say about CFAP96 p.Asp56Val (c.167A>T)?

AlphaMissense predicts likely benign (score 0.2195) — an in-silico prediction, not a clinical call.

CFAP96 p.Asp56Val

c.167A>T · rs1451160535 · VCV2398806

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2195 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00981%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2195	likely benign
REVEL	0.117	moderately benign-leaning
SaProt	LLR -4.58	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 -0.96	GERP -5.3
Regional constraint	o/e 0.92	unconstrained · MANE · 20 kb · p 0.15 · regional, not allelic
Overall
CADD	10.33	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 0.00981% Admixed American · 5/50,984 alleles

Filtering AF 0.00382% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00248%

Overall 0.000645% 10/1,551,586 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00981%	10,197
African / African-American	0.00274%	36,525
Remaining individualsnot grpmax-eligible	0.00166%	60,098
European (non-Finnish)	0.000174%	573,500

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: CFAP96
Protein: p.Asp56Val
Coding: c.167A>T
MANE Select: NM_001114357
dbSNP: rs1451160535
Type: single nucleotide variant
Location: chr4:185432048 (GRCh38)
Structure: AlphaFold pLDDT 74.34

Full CFAP96 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

UFSP2 p.Ile13Thr Uncertain significance ★★ ⚠ same type
UFSP2 p.Leu85Val Uncertain significance ★★ ⚠ same type
UFSP2 c.333+11T>C Benign ★★ same type
UFSP2 c.-33C>T Benign ★★ same type
UFSP2 p.Asn235Ser Benign/Likely benign ★★ same type
UFSP2 p.Glu93= Benign/Likely benign ★★ same type
UFSP2 p.Ser79= Benign ★★ same type
UFSP2 p.Thr76= 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/cfap96-p-asp56val (accessed [today's date]).

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