A1CF p.Cys76=
c.228T>C · rs35967725 · VCV781673
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.966%, 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 8.1 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 10.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.966%
South Asian · 877/90,820 alleles
Filtering AF
0.913%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.891%
Overall
0.764%
12,320/1,613,162 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.966% | 104 |
| European (non-Finnish) | 0.91% | 110 |
| Remaining individualsnot grpmax-eligible | 0.571% | 175 |
| Middle Eastern | 0.281% | 356 |
| Finnishnot grpmax-eligible | 0.219% | 457 |
| African / African-American | 0.129% | 773 |
| Admixed American | 0.122% | 821 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0676% | 1,479 |
| East Asian | 0.00223% | 44,856 |
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.Cys76=
- Coding
- c.228T>C
- MANE Select
- NM_014576
- dbSNP
- rs35967725
- Type
- single nucleotide variant
- Location
- chr10:50843994 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.70 · 1 PDB
- Residue 76
- the rrm 1 domain
Similar variants
- A1CF p.Ala195= Benign ★★ same type
- A1CF p.Gly390Ser Likely benign ★★ same type
- A1CF p.Ser294= 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-cys76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown