CCDC40 c.1159+239C>A
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 62.3%, 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 +239 | deep intronic (+239 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -0.38 |
| Non-coding constraint | Z 3.08 | 1 kb window · o/e 0.78 · regional · uncalibrated |
| Overall | ||
| CADD | 3.414 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
62.3%
African / African-American · 25,825/41,482 alleles
Filtering AF
61.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 61.4%
Overall
32%
48,632/152,122 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 62.3% | 2 |
| Remaining individualsnot grpmax-eligible | 29.1% | 3 |
| Middle Eastern | 26.9% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 23% | 4 |
| Finnishnot grpmax-eligible | 23% | 4 |
| South Asian | 23% | 4 |
| European (non-Finnish) | 20.7% | 5 |
| Admixed American | 17.8% | 6 |
| East Asian | 16.5% | 6 |
| Amishnot grpmax-eligible | 12.2% | 8 |
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
- CCDC40
- Coding
- c.1159+239C>A
- MANE Select
- NM_017950
- dbSNP
- rs9890752
- Type
- single nucleotide variant
- Location
- chr17:80050522 (GRCh38)
- Gene constraint
- LOEUF 0.962 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 71.70 · 1 PDB
Similar variants
- GAA p.Cys103Gly Pathogenic ★★★ same type
- CCDC40 c.1159+1G>A Likely pathogenic ★★ same type
- CCDC40 c.1440+1G>C Pathogenic/Likely pathogenic ★★ same type
- CCDC40 c.1989+1G>A Pathogenic/Likely pathogenic ★★ same type
- CCDC40 c.2712-1G>T Pathogenic/Likely pathogenic ★★ same type
- CCDC40 c.855+1G>A Pathogenic/Likely pathogenic ★★ same type
- CCDC40 c.940-1G>C Pathogenic/Likely pathogenic ★★ same type
- CCDC40 c.940-2A>G Pathogenic ★★ 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/ccdc40-c-1159-plus-239c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown