Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Common
common (popmax 26%, sas) — 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 -3.3 | GERP -3.5 |
| Overall | ||
| CADD | 0.308 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
26%
South Asian · 14,703/56,627 alleles
Filtering AF
25.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 25.5%
Overall
23.8%
287,492/1,206,924 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 26% | 4 |
| European (non-Finnish) | 24.9% | 4 |
| Admixed American | 24.9% | 4 |
| Middle Eastern | 24% | 4 |
| African / African-American | 22.9% | 4 |
| Remaining individualsnot grpmax-eligible | 22.9% | 4 |
| Finnishnot grpmax-eligible | 21% | 5 |
| Amishnot grpmax-eligible | 16.4% | 6 |
| Ashkenazi Jewishnot grpmax-eligible | 16% | 6 |
| East Asian | 1.5% | 67 |
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
- Protein
- p.Asn428=
- Coding
- c.1284C>T
- MANE Select
- NM_001145252
- dbSNP
- rs1048118
- Type
- single nucleotide variant
- Location
- chrX:47624401 (GRCh38)
- Structure
- AlphaFold pLDDT 83.75 · 14 PDB
- Residue 428
- a β-strand; a disulfide bond; the tsp type-1 6 domain
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-p-asn428 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown