CHD3 p.Val1292=
c.3876C>T · VCV3341837
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0736%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.36 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.079 | GERP -3.8, phastCons 0.52 |
| Overall | ||
| CADD | 9.329 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0736%
South Asian · 67/91,072 alleles
Filtering AF
0.0593%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0542%
Overall
0.00527%
85/1,614,014 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0736% | 1,359 |
| Middle Eastern | 0.0166% | 6,040 |
| African / African-American | 0.008% | 12,506 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,801 |
| European (non-Finnish) | 0.000763% | 131,104 |
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
- CHD3
- Protein
- p.Val1292=
- Coding
- c.3876C>T
- MANE Select
- NM_001005273
- Type
- single nucleotide variant
- Location
- chr17:7903973 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1292
- a UniProt-annotated variant site (in snibcps)
Similar variants
- CHD3 c.4073-2A>C Likely pathogenic ★★ same type
- CHD3 p.Arg103Ter Pathogenic ★★ same type
- CHD3 p.Arg1078Gln Pathogenic/Likely pathogenic ★★ same type
- CHD3 p.Arg1121Pro Pathogenic/Likely pathogenic ★★ same type
- CHD3 p.Arg1169Gln Pathogenic/Likely pathogenic ★★ same type
- CHD3 p.Arg1169Pro Pathogenic/Likely pathogenic ★★ same type
- CHD3 p.Arg1169Trp Pathogenic ★★ same type
- CHD3 p.Arg1172Gln Pathogenic/Likely pathogenic ★★ 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/chd3-p-val1292 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown