CFAP418 p.Asp152=
c.456T>C · rs1298964816 · VCV2981558
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00335%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.93 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP -0.88, phastCons 1 |
| Overall | ||
| CADD | 7.667 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00335%
Admixed American · 2/59,738 alleles
Filtering AF
0.000555%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000208%
Overall
0.000186%
3/1,612,238 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00335% | 29,869 |
| European (non-Finnish) | 8.48e-05% | 1,179,103 |
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
- CFAP418
- Protein
- p.Asp152=
- Coding
- c.456T>C
- MANE Select
- NM_177965
- dbSNP
- rs1298964816
- Type
- single nucleotide variant
- Location
- chr8:95252202 (GRCh38)
- Gene constraint
- LOEUF 1.642 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 75.73
Similar variants
- CFAP418 p.Arg177Trp Pathogenic/Likely pathogenic ★★ same type
- CFAP418 p.Trp147Ter Pathogenic/Likely pathogenic ★★ same type
- CFAP418 p.Trp185Ter Pathogenic/Likely pathogenic ★★ same type
- CFAP418 c.*408G>A Uncertain significance ★★ same type
- CFAP418 c.*965C>G Uncertain significance ★★ same type
- CFAP418 p.Ala178Val Uncertain significance ★★ ⚠ same type
- CFAP418 p.Ala45Gly Uncertain significance ★★ ⚠ same type
- CFAP418 p.Arg177Gln 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/cfap418-p-asp152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown