CHD3 p.Phe1154=
c.3462T>C · rs74903197 · VCV3038116
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.01%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.8 |
| Overall | ||
| CADD | 3.323 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.01%
East Asian · 1,801/44,878 alleles
Filtering AF
3.86%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.8%
Overall
0.133%
2,144/1,614,136 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 4.01% | 25 |
| Remaining individualsnot grpmax-eligible | 0.245% | 409 |
| Ashkenazi Jewishnot grpmax-eligible | 0.199% | 502 |
| South Asian | 0.0516% | 1,938 |
| Middle Eastern | 0.033% | 3,031 |
| Admixed American | 0.0317% | 3,159 |
| European (non-Finnish) | 0.005% | 20,000 |
| Finnishnot grpmax-eligible | 0.00312% | 32,016 |
| African / African-American | 0.00267% | 37,511 |
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.Phe1154=
- Coding
- c.3462T>C
- MANE Select
- NM_001005273
- dbSNP
- rs74903197
- Type
- single nucleotide variant
- Location
- chr17:7903028 (GRCh38)
- Gene constraint
- LOEUF 0.257 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.21
- Residue 1154
- the helicase c-terminal domain; 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-phe1154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown