A1CF p.Ser294=
c.882C>T · rs142026324 · VCV774682
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.576%, 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 0.048 | GERP -3.1, phastCons 0.44 |
| Overall | ||
| CADD | 10.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.576%
European (non-Finnish) · 6,795/1,179,590 alleles
Filtering AF
0.565%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.56%
Overall
0.449%
7,240/1,613,282 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.576% | 174 |
| Remaining individualsnot grpmax-eligible | 0.29% | 345 |
| Ashkenazi Jewishnot grpmax-eligible | 0.237% | 422 |
| African / African-American | 0.128% | 781 |
| Middle Eastern | 0.0661% | 1,514 |
| Admixed American | 0.0517% | 1,934 |
| Finnishnot grpmax-eligible | 0.0407% | 2,458 |
| South Asian | 0.0395% | 2,529 |
| East Asian | 0.00223% | 44,830 |
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
- A1CF
- Protein
- p.Ser294=
- Coding
- c.882C>T
- MANE Select
- NM_014576
- dbSNP
- rs142026324
- Type
- single nucleotide variant
- Location
- chr10:50816265 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.70 · 1 PDB
- Residue 294
- a β-strand; the rrm 3 domain
Similar variants
- A1CF p.Ala195= Benign ★★ same type
- A1CF p.Cys76= Benign ★★ same type
- A1CF p.Gly390Ser Likely benign ★★ same type
- A1CF c.100-6618G>A Uncertain significance ★ same type
- A1CF c.100-6622G>A Uncertain significance ★ same type
- A1CF p.Ala383Val Uncertain significance ★ ⚠ same type
- A1CF p.Ala462Ser Uncertain significance ★ ⚠ same type
- A1CF p.Ala497Ser 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/a1cf-p-ser294 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown