CFP c.*2A>T
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.09%, 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 -0.98 | GERP -3.5 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 0.867 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.09%
African / African-American · 617/56,795 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.987%
Overall
0.0598%
722/1,208,148 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.09% | 92 |
| Middle Eastern | 0.138% | 725 |
| Remaining individualsnot grpmax-eligible | 0.114% | 881 |
| Admixed American | 0.068% | 1,471 |
| South Asian | 0.0141% | 7,094 |
| European (non-Finnish) | 0.000671% | 149,048 |
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
- CFP
- Coding
- c.*2A>T
- MANE Select
- NM_001145252
- dbSNP
- rs138490907
- Type
- single nucleotide variant
- Location
- chrX:47624273 (GRCh38)
- Structure
- AlphaFold pLDDT 83.75 · 14 PDB
Similar variants
- CFP p.Trp321Gly Pathogenic ★★ same type
- CFP p.Ala402Gly Uncertain significance ★★ ⚠ same type
- CFP p.Arg157Gln Uncertain significance ★★ ⚠ same type
- CFP p.Arg157Trp Uncertain significance ★★ ⚠ same type
- CFP p.Arg159Cys Uncertain significance ★★ ⚠ same type
- CFP p.Arg247Trp Uncertain significance ★★ ⚠ same type
- CFP p.Arg438Trp Uncertain significance ★★ ⚠ same type
- CFP p.Asn307Ser 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/cfp-c-star-2a-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown