CTR9 c.45+45G>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 53.4%, eas) — 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 +45 | near-intronic (+45 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP -2.3, phastCons 0.077 |
| Non-coding constraint | Z 2.43 | 1 kb window · o/e 0.79 · regional · uncalibrated |
| Overall | ||
| CADD | 10.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
53.4%
East Asian · 23,795/44,590 alleles
Filtering AF
52.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 52.6%
Overall
39%
620,303/1,588,700 alleles · common
exomes 567,249/1,436,826 · genomes 53,054/151,874 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 53.4% | 2 |
| South Asian | 47.7% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 46.9% | 2 |
| Finnishnot grpmax-eligible | 42.2% | 2 |
| Middle Eastern | 40.8% | 2 |
| European (non-Finnish) | 39.2% | 3 |
| Remaining individualsnot grpmax-eligible | 38.7% | 3 |
| Amishnot grpmax-eligible | 35% | 3 |
| Admixed American | 27.1% | 4 |
| African / African-American | 22.3% | 4 |
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
- CTR9
- Coding
- c.45+45G>A
- MANE Select
- NM_014633
- dbSNP
- rs2279697
- Type
- single nucleotide variant
- Location
- chr11:10751502 (GRCh38)
- Gene constraint
- LOEUF 0.368 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.62 · 21 PDB
Similar variants
- CTR9 p.Asn455Ser Likely pathogenic ★★ same type
- CTR9 p.Ile17Thr Pathogenic/Likely pathogenic ★★ same type
- CTR9 p.Pro25Arg Pathogenic/Likely pathogenic ★★ same type
- CTR9 c.1960+3G>A Uncertain significance ★★ same type
- CTR9 c.2109+4A>G Uncertain significance ★★ same type
- CTR9 c.2445-3T>C Uncertain significance ★★ same type
- CTR9 c.45+5G>T Uncertain significance ★★ same type
- CTR9 c.593-8T>A 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/ctr9-c-45-plus-45g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown