CCNF c.594+87T>C
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 92.1%, 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 | ||
| Splice region | donor +87 | deep intronic (+87 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -1.4 |
| Overall | ||
| CADD | 2.693 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
92.1%
African / African-American · 58,267/63,274 alleles
Filtering AF
91.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 91.2%
Overall
70.8%
704,510/994,574 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 92.1% | 1 |
| East Asian | 86.6% | 1 |
| Admixed American | 81.8% | 1 |
| South Asian | 71.9% | 1 |
| Remaining individualsnot grpmax-eligible | 70.7% | 1 |
| European (non-Finnish) | 67.6% | 1 |
| Finnishnot grpmax-eligible | 64.4% | 2 |
| Middle Eastern | 62% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 60.7% | 2 |
| Amishnot grpmax-eligible | 55.8% | 2 |
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
- CCNF
- Coding
- c.594+87T>C
- MANE Select
- NM_001761
- dbSNP
- rs12926008
- Type
- single nucleotide variant
- Location
- chr16:2438210 (GRCh38)
- Gene constraint
- LOEUF 0.531 · pLI 0.70 (gnomAD)
- Structure
- AlphaFold pLDDT 72.34 · 1 PDB
Similar variants
- CCNF p.Ser621Gly Pathogenic/Likely pathogenic ★★ ⚠ same type
- CCNF p.Arg140Gln Uncertain significance ★★ ⚠ same type
- CCNF p.Arg24Lys Uncertain significance ★★ ⚠ same type
- CCNF p.Arg572Gln Uncertain significance ★★ ⚠ same type
- CCNF p.Gly254Ala Uncertain significance ★★ ⚠ same type
- CCNF p.Gly719Val Uncertain significance ★★ ⚠ same type
- CCNF c.1095-28A>G Benign ★★ same type
- CCNF c.1095-7G>A Benign ★★ 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/ccnf-c-594-plus-87t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown