CFAP92 p.His724=
c.2172C>T · rs200730768 · VCV2654115
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0821%, sas)
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 -0.089 | GERP -3.3, phastCons 0.088 |
| Overall | ||
| CADD | 2.045 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0821%
South Asian · 69/84,066 alleles
Filtering AF
0.0692%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0676%
Overall
0.0652%
1,001/1,536,170 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0821% | 1,218 |
| European (non-Finnish) | 0.0733% | 1,364 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0628% | 1,592 |
| Remaining individualsnot grpmax-eligible | 0.0533% | 1,876 |
| Admixed American | 0.0451% | 2,218 |
| Finnishnot grpmax-eligible | 0.0157% | 6,361 |
| African / African-American | 0.015% | 6,652 |
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
- CFAP92
- Protein
- p.His724=
- Coding
- c.2172C>T
- MANE Select
- NM_001394090
- dbSNP
- rs200730768
- Type
- single nucleotide variant
- Location
- chr3:128945157 (GRCh38)
- Gene constraint
- LOEUF 0.959 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.39
Similar variants
- ACAD9 c.1692+1G>A Likely pathogenic ★★ same type
- ACAD9 p.Arg532Gln Likely pathogenic ★★ ⚠ same type
- ACAD9 p.Asn569His Uncertain significance ★★ ⚠ same type
- ACAD9 p.Glu596Lys Uncertain significance ★★ ⚠ same type
- ACAD9 c.1692+145G>C Benign ★★ same type
- ACAD9 c.*26C>T Benign/Likely benign ★★ same type
- ACAD9 c.*331T>G Benign/Likely benign ★★ same type
- ACAD9 c.*68C>T Benign/Likely 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/cfap92-p-his724 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown