COL2A1 c.3003+9G>A
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 10 submitters
gnomAD v4.1
Rare
rare (popmax 0.55%, afr)
Conditions
2
type 2 collagenopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2 | GERP -0.8 |
| Non-coding constraint | Z 5.55 | 1 kb window · o/e 0.66 · regional · uncalibrated |
| Overall | ||
| CADD | 6.819 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.55%
African / African-American · 413/75,044 alleles
Filtering AF
0.507%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.489%
Overall
0.0291%
470/1,613,688 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.55% | 182 |
| Admixed American | 0.0433% | 2,308 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,500 |
| South Asian | 0.0011% | 91,050 |
| European (non-Finnish) | 0.000424% | 235,971 |
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
- COL2A1
- Coding
- c.3003+9G>A
- MANE Select
- NM_001844
- dbSNP
- rs200403247
- Type
- single nucleotide variant
- Location
- chr12:47978282 (GRCh38)
- Gene constraint
- LOEUF 0.183 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.56 · 11 PDB
Similar variants
- COL2A1 c.1222-2A>G Pathogenic ★★ same condition
- COL2A1 c.1365+1G>A Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 c.1420-2A>G Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 c.1527+135G>A Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 c.1581+1G>A Likely pathogenic ★★ same condition
- COL2A1 c.1833+1G>A Pathogenic ★★ same condition
- COL2A1 c.1887+1G>A Pathogenic/Likely pathogenic ★★ same condition
- COL2A1 c.1888-2A>C Pathogenic ★★ same condition
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/col2a1-c-3003-plus-9g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown