CHD6 p.Ser2247=
c.6741A>T · rs2515869790 · VCV2652333
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
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 -0.88 | GERP -4.8, phastCons 0.01 |
| Overall | ||
| CADD | 4.822 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,868 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,808 alleles · very rare
exomes 2/1,461,606 · genomes 0/152,202 · joint denominator
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.Ser2247=
- Coding
- c.6741A>T
- MANE Select
- NM_032221
- dbSNP
- rs2515869790
- Type
- single nucleotide variant
- Location
- chr20:41415384 (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-ser2247 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown