CHN1 p.Arg77=
c.231G>A · rs183170934 · VCV724251
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.181%, afr)
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 -0.59 | GERP -4, phastCons 0.001 |
| Overall | ||
| CADD | 3.849 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.181%
African / African-American · 136/75,006 alleles
Filtering AF
0.156%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.147%
Overall
0.00906%
146/1,612,012 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.181% | 552 |
| Admixed American | 0.01% | 9,975 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,812 |
| European (non-Finnish) | 8.48e-05% | 1,179,112 |
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
- CHN1
- Protein
- p.Arg77=
- Coding
- c.231G>A
- MANE Select
- NM_001822
- dbSNP
- rs183170934
- Type
- single nucleotide variant
- Location
- chr2:174915087 (GRCh38)
- Gene constraint
- LOEUF 0.79 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.41 · 2 PDB
- Residue 77
- the sh2 domain; a β-strand
Similar variants
- CHN1 c.-160C>G Uncertain significance ★★ same type
- CHN1 c.-74C>T Uncertain significance ★★ same type
- CHN1 p.Ala27Gly Uncertain significance ★★ ⚠ same type
- CHN1 p.Asp440Gly Uncertain significance ★★ ⚠ same type
- CHN1 p.Lys260Asn Uncertain significance ★★ ⚠ same type
- CHN1 p.Thr167Ile Uncertain significance ★★ ⚠ same type
- CHN1 p.Val65Met Uncertain significance ★★ ⚠ same type
- CHN1 c.886+15G>A 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/chn1-p-arg77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown