CHD7 p.Pro671=
c.2013G>A · rs1361271759 · VCV1554840
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0282%, eas)
Conditions
1
CHARGE syndrome
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 -1.3 | GERP -5.5 |
| Overall | ||
| CADD | 9.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0282%
East Asian · 12/42,608 alleles
Filtering AF
0.0163%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0127%
Overall
0.00121%
19/1,567,502 alleles · ultra-rare
exomes 18/1,415,392 · genomes 1/152,110 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0282% | 3,551 |
| African / African-American | 0.00138% | 72,432 |
| European (non-Finnish) | 0.000517% | 193,390 |
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
- CHD7
- Protein
- p.Pro671=
- Coding
- c.2013G>A
- MANE Select
- NM_017780
- dbSNP
- rs1361271759
- Type
- single nucleotide variant
- Location
- chr8:60781347 (GRCh38)
- Gene constraint
- LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 671
- the 'disordered' region
Similar variants
- CHD7 p.Pro671Leu Benign/Likely benign ★★ same residue
- CHD7 p.Pro671Ser Uncertain significance ★ same residue
- CHD7 p.Pro671Arg Likely benign ★ same residue
- CHD7 c.2097-2A>G Pathogenic ★★ same condition
- CHD7 c.2238+1G>A Pathogenic ★★ same condition
- CHD7 c.2377-1G>A Likely pathogenic ★★ same condition
- CHD7 c.2613+1G>A Pathogenic/Likely pathogenic ★★ same condition
- CHD7 c.2836-1G>A Pathogenic/Likely pathogenic ★★ 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/chd7-p-pro671 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown