Is CHD7 p.Pro2900= (c.8700G>A) pathogenic?

CHD7 p.Pro2900= (c.8700G>A) is classified Benign/Likely benign in CHD7 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-06). Very rare (popmax 0.00802%, afr); Associated with Inborn genetic diseases.

What condition is associated with CHD7 p.Pro2900= (c.8700G>A)?

CHD7 p.Pro2900= (c.8700G>A) is associated with Inborn genetic diseases, CHARGE syndrome (ClinVar).

How common is CHD7 p.Pro2900= (c.8700G>A) in the general population?

CHD7 p.Pro2900= (c.8700G>A) is very rare (popmax 0.00802%, afr) (gnomAD).

CHD7 p.Pro2900=

c.8700G>A · rs1320097712 · VCV1764371

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00802%, 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 -2.1	GERP -2.7
Overall
CADD	2.489	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00802% African / African-American · 6/74,800 alleles

Filtering AF 0.00348% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.000931% 15/1,611,556 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00802%	12,467
Remaining individualsnot grpmax-eligible	0.0016%	62,358
Finnishnot grpmax-eligible	0.00156%	63,934
European (non-Finnish)	0.000594%	168,310

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.Pro2900=
Coding: c.8700G>A
MANE Select: NM_017780
dbSNP: rs1320097712
Type: single nucleotide variant
Location: chr8:60865639 (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

Similar variants

CHD7 p.Pro2900Gln Uncertain significance ★ ⚠ same residue
CHD7 p.Pro2900Leu Uncertain significance ★ 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-pro2900 (accessed [today's date]).

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