CFH c.58+25T>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,546,058)
Conditions
4
age related macular degeneration 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +25 | near-intronic (+25 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4 | GERP -3.6 |
| Non-coding constraint | Z -3.42 | 1 kb window · o/e 1.27 · regional · uncalibrated |
| Overall | ||
| CADD | 0.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,546,058). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CFH
- Coding
- c.58+25T>C
- MANE Select
- NM_000186
- Type
- single nucleotide variant
- Location
- chr1:196652200 (GRCh38)
- Gene constraint
- LOEUF 0.43 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.54 · 51 PDB
Similar variants
- CFH c.1337-2A>G Likely pathogenic ★★ same condition
- CFH c.1520-1G>A Pathogenic/Likely pathogenic ★★ same condition
- CFH c.2236+1G>C Likely pathogenic ★★ same condition
- CFH c.3493+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CFH c.350+1G>T Pathogenic/Likely pathogenic ★★ same condition
- CFH c.619+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CFH p.Arg1215Leu Likely pathogenic ★★ ⚠ same condition
- CFH p.Arg1215Ter Pathogenic/Likely pathogenic ★★ same condition
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/cfh-c-58-plus-25t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown