CHD1 p.Pro1241=
c.3723A>G · VCV4971563
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.114%, amr)
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 Δ0.23 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3 | GERP -1 |
| Overall | ||
| CADD | 8.151 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.114%
Admixed American · 68/59,570 alleles
Filtering AF
0.0945%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0926%
Overall
0.0808%
1,303/1,612,006 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.114% | 876 |
| European (non-Finnish) | 0.0993% | 1,007 |
| Ashkenazi Jewishnot grpmax-eligible | 0.061% | 1,638 |
| Remaining individualsnot grpmax-eligible | 0.0449% | 2,229 |
| African / African-American | 0.0133% | 7,497 |
| Finnishnot grpmax-eligible | 0.0125% | 7,999 |
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
- CHD1
- Protein
- p.Pro1241=
- Coding
- c.3723A>G
- MANE Select
- NM_001270
- Type
- single nucleotide variant
- Location
- chr5:98872189 (GRCh38)
- Gene constraint
- LOEUF 0.207 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.63 · 18 PDB
Similar variants
- CHD1 p.Arg1378Gly Uncertain significance ★★ ⚠ same type
- CHD1 p.Arg1659Thr Uncertain significance ★★ ⚠ same type
- CHD1 p.Arg1676Gly Uncertain significance ★★ ⚠ same type
- CHD1 p.Arg1708Gln Uncertain significance ★★ same type
- CHD1 p.Arg1708Trp Uncertain significance ★★ ⚠ same type
- CHD1 p.Arg233His Uncertain significance ★★ same type
- CHD1 p.Arg70Ter Uncertain significance ★★ same type
- CHD1 p.Asn1518His Uncertain significance ★★ ⚠ 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/chd1-p-pro1241 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown