CFAP410 p.Arg196=
c.588G>A · rs147159770 · VCV747376
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.188%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.36 | GERP -1.1, phastCons 0.001 |
| Overall | ||
| CADD | 2.863 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.188%
Admixed American · 112/59,548 alleles
Filtering AF
0.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.149%
Overall
0.00792%
127/1,604,024 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.188% | 532 |
| Remaining individualsnot grpmax-eligible | 0.0145% | 6,886 |
| African / African-American | 0.00401% | 24,966 |
| European (non-Finnish) | 0.000256% | 391,285 |
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
- CFAP410
- Protein
- p.Arg196=
- Coding
- c.588G>A
- MANE Select
- NM_004928
- dbSNP
- rs147159770
- Type
- single nucleotide variant
- Location
- chr21:44330877 (GRCh38)
- Gene constraint
- LOEUF 1.453 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.77 · 1 PDB
- Residue 196
- the 'disordered' region
Similar variants
- CFAP410 p.Arg196Gln Uncertain significance ★★ ⚠ same residue
- CFAP410 p.Arg196Leu Uncertain significance ★ ⚠ same residue
- CFAP410 p.Arg196Trp Uncertain significance ★ ⚠ same residue
- CFAP410 c.545+1G>A Pathogenic ★★ same type
- CFAP410 c.642+2T>C Pathogenic ★★ same type
- CFAP410 c.643-1G>C Pathogenic ★★ same type
- CFAP410 c.643-23A>T Pathogenic/Likely pathogenic ★★ same type
- CFAP410 c.96+1G>A Pathogenic ★★ 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/cfap410-p-arg196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown