Is CFAP97 p.Ala510Val (c.1529C>T) pathogenic?

CFAP97 p.Ala510Val (c.1529C>T) is classified Likely benign in CFAP97 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-16). AlphaMissense: likely benign (0.0755); Ultra-rare (popmax 0.0369%, amr).

How common is CFAP97 p.Ala510Val (c.1529C>T) in the general population?

CFAP97 p.Ala510Val (c.1529C>T) is ultra-rare (popmax 0.0369%, amr) (gnomAD).

What do computational predictors say about CFAP97 p.Ala510Val (c.1529C>T)?

AlphaMissense predicts likely benign (score 0.0755) — an in-silico prediction, not a clinical call.

CFAP97 p.Ala510Val

c.1529C>T · rs192418727 · VCV2382779

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0755 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0369%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0755	likely benign
REVEL	0.012	strongly benign-leaning
SaProt	LLR -6.18	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 0.4	GERP -2.1
Regional constraint	o/e 1.06	unconstrained · MANE · 28 kb · p 0.14 · regional, not allelic
Overall
CADD	0.317	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 0.0369% Admixed American · 22/59,664 alleles

Filtering AF 0.0249% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.021%

Overall 0.00515% 83/1,611,684 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0369%	2,712
Middle Eastern	0.0165%	6,056
Remaining individualsnot grpmax-eligible	0.0128%	7,800
Ashkenazi Jewishnot grpmax-eligible	0.0102%	9,837
African / African-American	0.00533%	18,747
European (non-Finnish)	0.00373%	26,796
South Asian	0.00111%	90,382

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: CFAP97
Protein: p.Ala510Val
Coding: c.1529C>T
MANE Select: NM_020827
dbSNP: rs192418727
Type: single nucleotide variant
Location: chr4:185162868 (GRCh38)
Gene constraint: LOEUF 1.095 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 58.55
Residue 510: the 'disordered' region

Full CFAP97 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP97 p.Ala510= Likely benign ★ same residue
CFAP97 p.Glu383= Benign ★★ same type
CFAP97 p.Thr499Met Benign ★★ same type
CFAP97 p.Ala152Gly Uncertain significance ★ ⚠ same type
CFAP97 p.Ala448Thr Uncertain significance ★ ⚠ same type
CFAP97 p.Arg381Ser Uncertain significance ★ ⚠ same type
CFAP97 p.Arg389Gln Uncertain significance ★ ⚠ same type
CFAP97 p.Arg457His 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/cfap97-p-ala510val (accessed [today's date]).

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