Is CFAP70 p.Thr186Ala (c.556A>G) pathogenic?

CFAP70 p.Thr186Ala (c.556A>G) is classified Uncertain significance in CFAP70 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-04). AlphaMissense: likely benign (0.0572); Rare (popmax 0.105%, eas).

How common is CFAP70 p.Thr186Ala (c.556A>G) in the general population?

CFAP70 p.Thr186Ala (c.556A>G) is rare (popmax 0.105%, eas) (gnomAD).

What do computational predictors say about CFAP70 p.Thr186Ala (c.556A>G)?

AlphaMissense predicts likely benign (score 0.0572) — an in-silico prediction, not a clinical call.

CFAP70 p.Thr186Ala

c.556A>G · rs184423319 · VCV3143648

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0572 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.105%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0572	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -6.20	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 -12	GERP -4.8
Overall
CADD	0.138	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 0.105% East Asian · 47/44,884 alleles

Filtering AF 0.0808% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0725%

Overall 0.00787% 127/1,614,172 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.105%	955
European (non-Finnish)	0.00644%	15,527
Remaining individualsnot grpmax-eligible	0.0032%	31,255
African / African-American	0.00267%	37,519

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: CFAP70
Protein: p.Thr186Ala
Coding: c.556A>G
MANE Select: NM_001367801
dbSNP: rs184423319
Type: single nucleotide variant
Location: chr10:73345118 (GRCh38)
Gene constraint: LOEUF 0.75 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.55

Full CFAP70 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP70 p.His372Tyr Likely benign ★★ same type
CFAP70 p.Ala433Pro Uncertain significance ★ ⚠ same type
CFAP70 p.Ala759Glu Uncertain significance ★ ⚠ same type
CFAP70 p.Ala78Thr Uncertain significance ★ ⚠ same type
CFAP70 p.Ala7Pro Uncertain significance ★ ⚠ same type
CFAP70 p.Ala948Val Uncertain significance ★ ⚠ same type
CFAP70 p.Ala955Ser Uncertain significance ★ ⚠ same type
CFAP70 p.Arg1045Trp 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/cfap70-p-thr186ala (accessed [today's date]).

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