CFC1 p.Gly33=
c.99C>T · VCV4821832
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0136%, afr)
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 -0.41 | |
| Overall | ||
| CADD | 6.531 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0136%
African / African-American · 10/73,628 alleles
Filtering AF
0.00735%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00559%
Overall
0.00267%
43/1,608,010 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0136% | 7,363 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,462 |
| European (non-Finnish) | 0.00238% | 41,993 |
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
- CFC1
- Protein
- p.Gly33=
- Coding
- c.99C>T
- MANE Select
- NM_032545
- Type
- single nucleotide variant
- Location
- chr2:130598790 (GRCh38)
- Gene constraint
- LOEUF 0.586 · pLI 0.86 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 64.18
Similar variants
- CFC1 p.Gly33Ser Uncertain significance ★★ ⚠ same residue
- CFC1 p.Ala145Thr Benign ★★ same type
- CFC1 p.Arg47Gln Benign ★★ same type
- CFC1 p.Asn21= Benign/Likely benign ★★ same type
- CFC1 p.Asn21His Benign ★★ same type
- CFC1 p.Gly59Arg Likely benign ★★ same type
- CFC1 p.Leu202= Benign/Likely benign ★★ same type
- CFC1 p.Ala195Val 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/cfc1-p-gly33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown