CP c.2425+209A>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.39%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +209 | deep intronic (+209 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -2.2, phastCons 0.99 |
| Non-coding constraint | Z 1.55 | 1 kb window · o/e 0.87 · regional · uncalibrated |
| Overall | ||
| CADD | 10.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.39%
African / African-American · 579/41,566 alleles
Filtering AF
1.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.26%
Overall
0.401%
611/152,320 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.39% | 72 |
| Remaining individualsnot grpmax-eligible | 0.189% | 528 |
| Admixed American | 0.15% | 665 |
| South Asian | 0.0207% | 4,832 |
| European (non-Finnish) | 0.00588% | 17,007 |
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
- CP
- Coding
- c.2425+209A>G
- MANE Select
- NM_000096
- dbSNP
- rs150167647
- Type
- single nucleotide variant
- Location
- chr3:149183257 (GRCh38)
- Gene constraint
- LOEUF 0.624 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.79 · 4 PDB
Similar variants
- CP c.1208+1G>A Pathogenic ★★ same type
- CP c.2879-1G>T Likely pathogenic ★★ same type
- CP p.Arg901Ter Pathogenic ★★ same type
- CP p.Gly195Arg Likely pathogenic ★★ same type
- CP p.Gly650Arg Pathogenic/Likely pathogenic ★★ same type
- CP p.Gly708Ser Pathogenic ★★ same type
- CP p.Leu919Pro Pathogenic/Likely pathogenic ★★ same type
- CP p.Val219Glu 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/cp-c-2425-plus-209a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown