CTR9 c.2580+79C>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 18.3%, 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 +79 | deep intronic (+79 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -1.1 |
| Non-coding constraint | Z 2.21 | 1 kb window · o/e 0.85 · regional · uncalibrated |
| Overall | ||
| CADD | 0.527 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
18.3%
East Asian · 6,978/38,104 alleles
Filtering AF
18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.8%
Overall
5.46%
74,852/1,370,954 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 18.3% | 5 |
| African / African-American | 17.8% | 6 |
| Amishnot grpmax-eligible | 14.7% | 7 |
| South Asian | 13.2% | 8 |
| Admixed American | 9.43% | 11 |
| Remaining individualsnot grpmax-eligible | 6.48% | 15 |
| Middle Eastern | 5.94% | 17 |
| Ashkenazi Jewishnot grpmax-eligible | 5.57% | 18 |
| European (non-Finnish) | 3.66% | 27 |
| Finnishnot grpmax-eligible | 2.99% | 33 |
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.2580+79C>A
- MANE Select
- NM_014633
- dbSNP
- rs11042957
- Type
- single nucleotide variant
- Location
- chr11:10772734 (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-2580-plus-79c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown