CHD3 p.Asp1713=
c.5139T>C · rs150988632 · VCV3053423
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.56%, eas)
Conditions
1
CHD3-related disorder
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 · T>A here scores Δ0.43 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.4 | GERP -3.2 |
| Overall | ||
| CADD | 1.926 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.56%
East Asian · 694/44,620 alleles
Filtering AF
1.46%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.42%
Overall
0.0459%
737/1,604,714 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.56% | 64 |
| Remaining individualsnot grpmax-eligible | 0.0532% | 1,878 |
| Middle Eastern | 0.0166% | 6,026 |
| South Asian | 0.00441% | 22,667 |
| Admixed American | 0.00168% | 59,596 |
| Finnishnot grpmax-eligible | 0.00156% | 63,948 |
| European (non-Finnish) | 0.000256% | 390,898 |
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.Asp1713=
- Coding
- c.5139T>C
- MANE Select
- NM_001005273
- dbSNP
- rs150988632
- Type
- single nucleotide variant
- Location
- chr17:7908006 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1713
- the 'required for interaction with pcnt' region; a UniProt-annotated variant site (in snibcps)
Disease context
CHD3-related disorder
Similar variants
- CHD3 p.Arg1172Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg1342Gln Pathogenic/Likely pathogenic ★★ same condition
- CHD3 p.Arg985Gln Pathogenic ★★ same condition
- CHD3 p.Arg1491His Uncertain significance ★★ ⚠ same condition
- CHD3 p.Arg684Ter Pathogenic ★ same condition
- CHD3 p.Glu1653Ter Likely pathogenic ★ same condition
- CHD3 p.Met1085Ile Likely pathogenic ★ same condition
- CHD3 p.Ala1289Thr Conflicting classifications of pathogenicity ★ ⚠ same condition
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-asp1713 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown