CFAP298 p.Ser12=
c.36C>T · rs752937858 · VCV702687
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00136%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.3 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 14.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00136%
European (non-Finnish) · 16/1,176,658 alleles
Filtering AF
0.000805%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000651%
Overall
0.000996%
16/1,606,914 alleles · very rare
exomes 16/1,455,574 · genomes 0/151,340 · joint denominator
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.Ser12=
- Coding
- c.36C>T
- MANE Select
- NM_021254
- dbSNP
- rs752937858
- Type
- single nucleotide variant
- Location
- chr21:32612208 (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-ser12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown