CFB c.64+15C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +15 | near-intronic (+15 nt from the splice site) |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.79 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.4 | GERP -1.1 |
| Non-coding constraint | Z 6.40 | 1 kb window · o/e 0.59 · regional · uncalibrated |
| Overall | ||
| CADD | 4.668 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,928 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,612,976 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,928 |
| European (non-Finnish) | 0.000169% | 590,023 |
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
- CFB
- Coding
- c.64+15C>A
- MANE Select
- NM_001710
- Type
- single nucleotide variant
- Location
- chr6:31946300 (GRCh38)
- Gene constraint
- LOEUF 0.719 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.54 · 28 PDB
Similar variants
- CFB c.2140-1G>C Uncertain significance ★★ same type
- CFB c.-3G>A Uncertain significance ★★ same type
- CFB p.Ala162Val Uncertain significance ★★ ⚠ same type
- CFB p.Ala289Val Uncertain significance ★★ ⚠ same type
- CFB p.Ala567Gly Uncertain significance ★★ ⚠ same type
- CFB p.Arg117Trp Uncertain significance ★★ ⚠ same type
- CFB p.Arg138Gln Uncertain significance ★★ ⚠ same type
- CFB p.Arg138Trp 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/cfb-c-64-plus-15c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown