CCNF c.540+3G>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.138%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.25 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -3.7, phastCons 1 |
| Non-coding constraint | Z 1.62 | 1 kb window · o/e 0.84 · regional · uncalibrated |
| Overall | ||
| CADD | 12.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.138%
South Asian · 122/88,270 alleles
Filtering AF
0.118%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.111%
Overall
0.00799%
126/1,577,026 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.138% | 724 |
| Remaining individualsnot grpmax-eligible | 0.00655% | 15,277 |
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.540+3G>A
- MANE Select
- NM_001761
- dbSNP
- rs772207315
- Type
- single nucleotide variant
- Location
- chr16:2437325 (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-540-plus-3g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown