Is CHD7 p.Pro548= (c.1644G>A) pathogenic?

CHD7 p.Pro548= (c.1644G>A) is classified Conflicting classifications of pathogenicity in CHD7 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-09-04). Very rare (popmax 0.008%, afr); Associated with Inborn genetic diseases.

What condition is associated with CHD7 p.Pro548= (c.1644G>A)?

CHD7 p.Pro548= (c.1644G>A) is associated with Inborn genetic diseases, CHARGE syndrome (ClinVar).

How common is CHD7 p.Pro548= (c.1644G>A) in the general population?

CHD7 p.Pro548= (c.1644G>A) is very rare (popmax 0.008%, afr) (gnomAD).

CHD7 p.Pro548=

c.1644G>A · rs748842029 · VCV195335

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.008%, afr)

Conditions

Inborn genetic diseases

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 0.91	GERP -1.4, phastCons 1
Overall
CADD	13.22	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.008% African / African-American · 6/75,046 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00228%

Overall 0.00136% 22/1,613,444 alleles · very rare exomes 17/1,461,148 · genomes 5/152,296 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.008%	12,508
Admixed American	0.00334%	29,983
East Asian	0.00223%	44,860
South Asian	0.0022%	45,477
Finnishnot grpmax-eligible	0.00157%	63,868
European (non-Finnish)	0.000848%	117,969

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.Pro548=
Coding: c.1644G>A
MANE Select: NM_017780
dbSNP: rs748842029
Type: single nucleotide variant
Location: chr8:60743076 (GRCh38)
Gene constraint: LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 548: the 'disordered' region

Full CHD7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: CHARGE syndrome

Similar variants

CHD7 p.Pro548Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
CHD7 p.Pro548Ser 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
CHD7 c.2836-2A>T 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-pro548 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown