CTR9 c.849+20A>G
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000189%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +20 | near-intronic (+20 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP 0.41, phastCons 0.007 |
| Non-coding constraint | Z 0.53 | 1 kb window · o/e 0.95 · regional · uncalibrated |
| Overall | ||
| CADD | 14.97 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000189%
European (non-Finnish) · 2/1,059,694 alleles
Filtering AF
3.1e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.2e-05%
Overall
0.000138%
2/1,451,860 alleles · very rare
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.849+20A>G
- MANE Select
- NM_014633
- dbSNP
- rs1243579006
- Type
- single nucleotide variant
- Location
- chr11:10762074 (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-849-plus-20a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown