Is CHD7 p.Ser1074= (c.3222C>T) pathogenic?

CHD7 p.Ser1074= (c.3222C>T) is classified Benign/Likely benign in CHD7 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-19). Ultra-rare (popmax 0.0439%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CHD7 p.Ser1074= (c.3222C>T)?

CHD7 p.Ser1074= (c.3222C>T) is associated with Inborn genetic diseases, CHARGE syndrome (ClinVar).

How common is CHD7 p.Ser1074= (c.3222C>T) in the general population?

CHD7 p.Ser1074= (c.3222C>T) is ultra-rare (popmax 0.0439%, nfe) (gnomAD).

CHD7 p.Ser1074=

c.3222C>T · rs199675568 · VCV363458

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0439%, nfe)

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 1	GERP 1.1, phastCons 1
Overall
CADD	9.883	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0439% European (non-Finnish) · 518/1,179,686 alleles

Filtering AF 0.0408% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0395%

Overall 0.0335% 541/1,613,670 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0439%	2,277
Remaining individualsnot grpmax-eligible	0.0176%	5,680
African / African-American	0.0107%	9,375
Finnishnot grpmax-eligible	0.00469%	21,329
Admixed American	0.00167%	59,984

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.Ser1074=
Coding: c.3222C>T
MANE Select: NM_017780
dbSNP: rs199675568
Type: single nucleotide variant
Location: chr8:60823860 (GRCh38)
Gene constraint: LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1074: the helicase atp-binding domain

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 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
CHD7 c.2957+2T>C Pathogenic ★★ same condition
CHD7 c.3202-3T>G 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-ser1074 (accessed [today's date]).

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