CBX2 c.72+25del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0281%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +25 | near-intronic (+25 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -4.1 | GERP -3.3 |
| Non-coding constraint | Z 4.77 | 1 kb window · o/e 0.73 · regional · uncalibrated |
| Overall | ||
| CADD | 4.439 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (GCCC)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0281%
East Asian · 12/42,656 alleles
Filtering AF
0.0161%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0127%
Overall
0.00283%
40/1,411,214 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0281% | 3,555 |
| South Asian | 0.00579% | 17,258 |
| Admixed American | 0.00536% | 18,661 |
| Remaining individualsnot grpmax-eligible | 0.00331% | 30,234 |
| African / African-American | 0.00275% | 36,393 |
| Finnishnot grpmax-eligible | 0.00199% | 50,302 |
| European (non-Finnish) | 0.00129% | 77,276 |
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
- CBX2
- Coding
- c.72+25del
- MANE Select
- NM_005189
- dbSNP
- rs781870900
- Type
- Deletion
- Location
- chr17:79778327 (GRCh38)
- Gene constraint
- LOEUF 0.946 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 57.29 · 3 PDB
Similar variants
- CBX2 c.117-18del Uncertain significance ★★ same type
- CBX2 c.288+37del Uncertain significance ★ same type
- CBX2 p.Cys89fs Uncertain significance ★ same type
- CBX2 p.Lys379_Thr384del Uncertain significance ★ same type
- CBX2 c.288+172del Likely benign ★ same type
- CBX2 c.289-17del Likely benign ★ 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/cbx2-c-72-plus-25del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown