CFAP74 p.Ala1340=
c.4020G>A · VCV4820837
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.36%, nfe)
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 -20 | GERP -2.9 |
| Overall | ||
| CADD | 0.031 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.36%
European (non-Finnish) · 4,246/1,179,914 alleles
Filtering AF
0.351%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.347%
Overall
0.294%
4,738/1,612,694 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.36% | 278 |
| Remaining individualsnot grpmax-eligible | 0.285% | 351 |
| South Asian | 0.216% | 462 |
| Middle Eastern | 0.116% | 865 |
| Admixed American | 0.0983% | 1,017 |
| African / African-American | 0.0573% | 1,746 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,400 |
| Finnishnot grpmax-eligible | 0.00478% | 20,899 |
| East Asian | 0.00223% | 44,890 |
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
- CFAP74
- Protein
- p.Ala1340=
- Coding
- c.4020G>A
- MANE Select
- NM_001304360
- Type
- single nucleotide variant
- Location
- chr1:1925867 (GRCh38)
- Gene constraint
- LOEUF 0.799 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.38
Similar variants
- CFAP74 p.Lys394Met Uncertain significance ★★ ⚠ same type
- CFAP74 p.Arg365Gln Likely benign ★★ same type
- CFAP74 p.Gly5Ser Likely benign ★★ same type
- CFAP74 p.Arg280Ter Likely pathogenic ★ same type
- CFAP74 c.1851+2T>C Uncertain significance ★ same type
- CFAP74 c.2176+30T>G Uncertain significance ★ same type
- CFAP74 c.2176+34C>T Uncertain significance ★ same type
- CFAP74 c.785+1G>A 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/cfap74-p-ala1340 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown