CHD3 c.*31C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.233%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.032 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP 0.4, phastCons 1 |
| Non-coding constraint | Z 5.41 | 1 kb window · o/e 0.67 · regional · uncalibrated |
| Overall | ||
| CADD | 16.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.233%
European (non-Finnish) · 2,754/1,179,580 alleles
Filtering AF
0.226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.223%
Overall
0.177%
2,851/1,613,394 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.233% | 428 |
| Remaining individualsnot grpmax-eligible | 0.08% | 1,249 |
| Finnishnot grpmax-eligible | 0.0329% | 3,043 |
| African / African-American | 0.032% | 3,126 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,594 |
| Admixed American | 0.00167% | 59,986 |
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
- Coding
- c.*31C>A
- MANE Select
- NM_001005273
- dbSNP
- rs201176893
- Type
- single nucleotide variant
- Location
- chr17:7911616 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
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-c-star-31c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown