CHD1L p.Ser283=
c.849A>C · rs111296687 · VCV3057589
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.292%, eas)
Conditions
1
CHD1L-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 -0.35 | GERP -3.3, phastCons 0.001 |
| Overall | ||
| CADD | 5.151 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.292%
East Asian · 131/44,858 alleles
Filtering AF
0.251%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.236%
Overall
0.00837%
135/1,613,764 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.292% | 342 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,623 |
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
- CHD1L
- Protein
- p.Ser283=
- Coding
- c.849A>C
- MANE Select
- NM_004284
- dbSNP
- rs111296687
- Type
- single nucleotide variant
- Location
- chr1:147266041 (GRCh38)
- Gene constraint
- LOEUF 1.152 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.81 · 7 PDB
Disease context
CHD1L-related disorder
Similar variants
- CHD1L p.Gln594Pro Uncertain significance ★★ same condition
- CHD1L p.Gln594His Uncertain significance ★ ⚠ same condition
- CHD1L p.Ser420Asn Uncertain significance ⚠ same condition
- CHD1L c.1386-2A>G Likely benign same condition
- CHD1L p.Arg37= Likely benign same condition
- CHD1L p.Arg663Lys Likely benign same condition
- CHD1L p.Gln549= Likely benign same condition
- CHD1L p.Leu57= Likely benign 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/chd1l-p-ser283 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown