CFAP298 p.Val90=
c.270G>A · rs111591095 · VCV413306
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.57%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.068 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -3 |
| Overall | ||
| CADD | 0.061 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.57%
African / African-American · 1,177/75,044 alleles
Filtering AF
1.49%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.46%
Overall
0.109%
1,766/1,614,088 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.57% | 64 |
| Middle Eastern | 0.182% | 551 |
| Remaining individualsnot grpmax-eligible | 0.181% | 553 |
| Admixed American | 0.117% | 857 |
| South Asian | 0.0538% | 1,859 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0304% | 3,289 |
| European (non-Finnish) | 0.0286% | 3,501 |
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
- CFAP298
- Protein
- p.Val90=
- Coding
- c.270G>A
- MANE Select
- NM_021254
- dbSNP
- rs111591095
- Type
- single nucleotide variant
- Location
- chr21:32609875 (GRCh38)
- Gene constraint
- LOEUF 1.267 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.54
Similar variants
- CFAP298 p.Arg98Ter Pathogenic/Likely pathogenic ★★ same type
- CFAP298 p.Gln225Ter Pathogenic ★★ same type
- CFAP298 p.Asp141Gly Uncertain significance ★★ ⚠ same type
- CFAP298 p.Gln225Arg Uncertain significance ★★ ⚠ same type
- CFAP298 p.Gly80Ser Uncertain significance ★★ ⚠ same type
- CFAP298 c.308-16C>G Benign ★★ same type
- CFAP298 c.375+15A>G Likely benign ★★ same type
- CFAP298 c.376-20C>T 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/cfap298-p-val90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown