CTR9 c.502+68G>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 19.1%, afr) — 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 +68 | deep intronic (+68 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.056 | GERP -3.3, phastCons 0.003 |
| Non-coding constraint | Z 3.43 | 1 kb window · o/e 0.75 · regional · uncalibrated |
| Overall | ||
| CADD | 0.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
19.1%
African / African-American · 11,210/58,612 alleles
Filtering AF
18.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 18.7%
Overall
4.81%
41,259/858,398 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 19.1% | 5 |
| East Asian | 18.3% | 5 |
| South Asian | 12.5% | 8 |
| Admixed American | 8.59% | 12 |
| Remaining individualsnot grpmax-eligible | 5.14% | 19 |
| Ashkenazi Jewishnot grpmax-eligible | 3.45% | 29 |
| Middle Eastern | 3.31% | 30 |
| European (non-Finnish) | 1.54% | 65 |
| Finnishnot grpmax-eligible | 1.09% | 92 |
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.502+68G>A
- MANE Select
- NM_014633
- dbSNP
- rs2270621
- Type
- single nucleotide variant
- Location
- chr11:10755863 (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-502-plus-68g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown