Is CHD7 p.Ser2373= (c.7119C>T) pathogenic?

CHD7 p.Ser2373= (c.7119C>T) is classified Likely benign in CHD7 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-23). Ultra-rare (popmax 0.0526%, amr); Associated with Inborn genetic diseases.

What condition is associated with CHD7 p.Ser2373= (c.7119C>T)?

CHD7 p.Ser2373= (c.7119C>T) is associated with Inborn genetic diseases, CHARGE syndrome, hypogonadotropic hypogonadism 5 with or without anosmia (ClinVar).

How common is CHD7 p.Ser2373= (c.7119C>T) in the general population?

CHD7 p.Ser2373= (c.7119C>T) is ultra-rare (popmax 0.0526%, amr) (gnomAD).

CHD7 p.Ser2373=

c.7119C>T · rs201046385 · VCV1132076

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0526%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.82	GERP 0.16
Overall
CADD	4.181	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0526% Admixed American · 31/58,890 alleles

Filtering AF 0.0381% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0331%

Overall 0.00249% 40/1,605,934 alleles · ultra-rare exomes 19/1,453,658 · genomes 21/152,276 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0526%	1,900
Remaining individualsnot grpmax-eligible	0.0129%	7,780
African / African-American	0.00134%	74,862

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.Ser2373=
Coding: c.7119C>T
MANE Select: NM_017780
dbSNP: rs201046385
Type: single nucleotide variant
Location: chr8:60856157 (GRCh38)
Gene constraint: LOEUF 0.109 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

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 hypogonadotropic hypogonadism 5 with or without anosmia

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-ser2373 (accessed [today's date]).

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