CHMP2B p.Ser84=
c.252T>C · VCV3351186
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0441%, afr)
Conditions
1
CHMP2B-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -0.18, phastCons 1 |
| Overall | ||
| CADD | 9.632 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0441%
African / African-American · 33/74,912 alleles
Filtering AF
0.0322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0281%
Overall
0.00204%
33/1,613,706 alleles · ultra-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
- CHMP2B
- Protein
- p.Ser84=
- Coding
- c.252T>C
- MANE Select
- NM_014043
- Type
- single nucleotide variant
- Location
- chr3:87245839 (GRCh38)
- Gene constraint
- LOEUF 1.503 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.26 · 1 PDB
Disease context
CHMP2B-related disorder
Similar variants
- CHMP2B p.Arg186Gln Uncertain significance ★ ⚠ same condition
- CHMP2B p.Met125Thr Uncertain significance ★ ⚠ same condition
- CHMP2B p.Thr108Ile Uncertain significance ★ ⚠ same condition
- CHMP2B p.Asp11Gly Uncertain significance ⚠ same condition
- CHMP2B p.Gln25Ter Uncertain significance same condition
- CHMP2B p.Arg186Ter Likely benign same condition
- CHMP2B p.Gln41fs Uncertain significance ★ same condition
- CHMP2B c.126+4A>G 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/chmp2b-p-ser84 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown