CPAP c.974+9C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0257%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.63 | GERP -2.5 |
| Overall | ||
| CADD | 6.276 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0257%
African / African-American · 19/74,032 alleles
Filtering AF
0.0168%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0139%
Overall
0.00365%
57/1,562,928 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0257% | 3,896 |
| Remaining individualsnot grpmax-eligible | 0.023% | 4,345 |
| Admixed American | 0.00834% | 11,984 |
| European (non-Finnish) | 0.00167% | 59,712 |
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
- CPAP
- Coding
- c.974+9C>T
- MANE Select
- NM_018451
- dbSNP
- rs376071108
- Type
- single nucleotide variant
- Location
- chr13:24908009 (GRCh38)
- Structure
- AlphaFold pLDDT 56.70 · 6 PDB
Similar variants
- CPAP c.2693-2A>G Likely pathogenic ★★ same type
- CPAP p.Arg1298Gln Likely pathogenic ★★ same type
- CPAP p.Arg378Ter Pathogenic ★★ same type
- CPAP p.Arg566Ter Pathogenic/Likely pathogenic ★★ same type
- CPAP p.Arg902Ter Pathogenic/Likely pathogenic ★★ same type
- CPAP p.Arg958Ter Pathogenic/Likely pathogenic ★★ same type
- CPAP p.Gln14Ter Pathogenic/Likely pathogenic ★★ same type
- CPAP p.Gln657Ter Pathogenic/Likely 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/cpap-c-974-plus-9c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown