CHN2 p.Asp110=
c.330C>T · VCV4228251
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, sas)
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 -0.76 | GERP -3.4, phastCons 0.02 |
| Overall | ||
| CADD | 8.928 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
South Asian · 15/91,086 alleles
Filtering AF
0.0101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00811%
Overall
0.00229%
37/1,614,002 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0165% | 6,072 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| European (non-Finnish) | 0.00161% | 62,107 |
| African / African-American | 0.00134% | 74,886 |
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
- CHN2
- Protein
- p.Asp110=
- Coding
- c.330C>T
- MANE Select
- NM_004067
- Type
- single nucleotide variant
- Location
- chr7:29400582 (GRCh38)
- Gene constraint
- LOEUF 0.885 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.06 · 1 PDB
- Residue 110
- the sh2 domain; a β-strand
Similar variants
- CHN2 p.Ala201Val Uncertain significance ★ ⚠ same type
- CHN2 p.Ala3Thr Uncertain significance ★ ⚠ same type
- CHN2 p.Arg290Ser Uncertain significance ★ ⚠ same type
- CHN2 p.Arg299Gln Uncertain significance ★ ⚠ same type
- CHN2 p.Arg313Thr Uncertain significance ★ ⚠ same type
- CHN2 p.Arg39His Uncertain significance ★ ⚠ same type
- CHN2 p.Arg404Trp Uncertain significance ★ ⚠ same type
- CHN2 p.Arg47Gln 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/chn2-p-asp110 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown