CRPPA c.933+207C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.91%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +207 | deep intronic (+207 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP 0.85 |
| Overall | ||
| CADD | 0.679 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.91%
African / African-American · 1,622/41,470 alleles
Filtering AF
3.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.69%
Overall
1.12%
1,710/152,054 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.91% | 26 |
| Remaining individualsnot grpmax-eligible | 0.758% | 132 |
| Admixed American | 0.393% | 254 |
| Middle Eastern | 0.34% | 294 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0865% | 1,157 |
| European (non-Finnish) | 0.0118% | 8,500 |
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
- CRPPA
- Coding
- c.933+207C>A
- MANE Select
- NM_001101426
- dbSNP
- rs114323347
- Type
- single nucleotide variant
- Location
- chr7:16277922 (GRCh38)
- Gene constraint
- LOEUF 1.462 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.63 · 1 PDB
Similar variants
- CRPPA c.1120-1G>T Pathogenic ★★ same type
- CRPPA c.258-1G>C Pathogenic/Likely pathogenic ★★ same type
- CRPPA c.835+2T>C Pathogenic/Likely pathogenic ★★ same type
- CRPPA p.Arg184Ter Pathogenic ★★ same type
- CRPPA p.Arg205Cys Likely pathogenic ★★ same type
- CRPPA p.Arg268Ter Pathogenic ★★ same type
- CRPPA p.Gln215Ter Pathogenic/Likely pathogenic ★★ same type
- CRPPA c.1026+5G>C Uncertain significance ★★ 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/crppa-c-933-plus-207c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown