CHD3 p.Asp1275=
c.3825C>T · rs61744840 · VCV770796
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, nfe)
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 -9.7 | GERP -2.5 |
| Overall | ||
| CADD | 2.663 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
European (non-Finnish) · 14,696/1,180,010 alleles
Filtering AF
1.23%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.22%
Overall
1.04%
16,741/1,614,156 alleles · low-frequency
exomes 15,626/1,461,862 · genomes 1,115/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.25% | 80 |
| Remaining individualsnot grpmax-eligible | 0.891% | 112 |
| Ashkenazi Jewishnot grpmax-eligible | 0.824% | 121 |
| Finnishnot grpmax-eligible | 0.614% | 163 |
| South Asian | 0.508% | 197 |
| Middle Eastern | 0.462% | 216 |
| Admixed American | 0.343% | 291 |
| African / African-American | 0.199% | 504 |
| East Asian | 0.0111% | 8,977 |
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.Asp1275=
- Coding
- c.3825C>T
- MANE Select
- NM_001005273
- dbSNP
- rs61744840
- Type
- single nucleotide variant
- Location
- chr17:7903922 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1275
- a UniProt-annotated variant site (in snibcps)
Similar variants
- CHD3 p.Asp1275Glu Uncertain significance ★ ⚠ same residue
- 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
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-asp1275 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown