CFC1 p.Leu202=
c.606G>C · rs587780887 · VCV136738
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Common
common (popmax 6.72%, afr) — too common for a highly-penetrant pathogenic allele
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 -1.8 | |
| Overall | ||
| CADD | 1.161 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.72%
African / African-American · 1,527/22,738 alleles
Filtering AF
6.44%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.32%
Overall
0.391%
1,927/492,400 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 6.72% | 15 |
| Admixed American | 0.761% | 131 |
| Remaining individualsnot grpmax-eligible | 0.612% | 163 |
| Middle Eastern | 0.328% | 305 |
| European (non-Finnish) | 0.0193% | 5,172 |
| South Asian | 0.0111% | 9,031 |
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.Leu202=
- Coding
- c.606G>C
- MANE Select
- NM_032545
- dbSNP
- rs587780887
- Type
- single nucleotide variant
- Location
- chr2:130592943 (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 type
- 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.Ala195Val Uncertain significance ★ ⚠ same type
- CFC1 p.Ala79Thr 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-leu202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown