CHD6 p.Pro1209=
c.3627C>T · rs41278124 · VCV724654
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.271%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.241 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.5 | GERP -5.1 |
| Overall | ||
| CADD | 1.654 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.271%
European (non-Finnish) · 3,200/1,179,840 alleles
Filtering AF
0.263%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.26%
Overall
0.208%
3,361/1,613,932 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.271% | 369 |
| Remaining individualsnot grpmax-eligible | 0.107% | 933 |
| Finnishnot grpmax-eligible | 0.0671% | 1,489 |
| African / African-American | 0.0373% | 2,680 |
| Admixed American | 0.0367% | 2,728 |
| Middle Eastern | 0.0165% | 6,060 |
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
- CHD6
- Protein
- p.Pro1209=
- Coding
- c.3627C>T
- MANE Select
- NM_032221
- dbSNP
- rs41278124
- Type
- single nucleotide variant
- Location
- chr20:41451002 (GRCh38)
- Gene constraint
- LOEUF 0.221 · pLI 1.00 (gnomAD)
Similar variants
- CHD6 c.1858-19G>A Benign ★★ same type
- CHD6 c.554+5G>A Benign/Likely benign ★★ same type
- CHD6 c.852+4T>C Benign ★★ same type
- CHD6 p.Ala1205Gly Benign ★★ same type
- CHD6 p.Arg2389Cys Benign ★★ same type
- CHD6 p.Glu1271= Benign ★★ same type
- CHD6 p.Glu2404Gln Benign ★★ same type
- CHD6 p.Gly1519Asp Benign ★★ 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/chd6-p-pro1209 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown