CFAP74 p.Ser617=
c.1851G>A · rs146150343 · VCV3057108
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.4%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.012 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.71 | donor loss at this position · masked 0 · deltas |
| Pangolin | Δ0.71 | loss · gain 0.06 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -5.6 | GERP -3.2 |
| Overall | ||
| CADD | 4.409 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.4%
South Asian · 364/90,930 alleles
Filtering AF
0.366%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.353%
Overall
0.281%
4,521/1,608,520 alleles · rare
exomes 4,154/1,456,268 · genomes 367/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.4% | 250 |
| European (non-Finnish) | 0.314% | 319 |
| Remaining individualsnot grpmax-eligible | 0.268% | 373 |
| Admixed American | 0.252% | 397 |
| African / African-American | 0.139% | 721 |
| Middle Eastern | 0.116% | 864 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0507% | 1,971 |
| Finnishnot grpmax-eligible | 0.0362% | 2,765 |
| East Asian | 0.00446% | 22,424 |
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.Ser617=
- Coding
- c.1851G>A
- MANE Select
- NM_001304360
- dbSNP
- rs146150343
- Type
- single nucleotide variant
- Location
- chr1:1959120 (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-ser617 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown