Is CHD5 p.Ala1889= (c.5667C>T) pathogenic?

CHD5 p.Ala1889= (c.5667C>T) is classified Likely benign in CHD5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-17). Ultra-rare (popmax 0.0446%, eas); Associated with Inborn genetic diseases.

What condition is associated with CHD5 p.Ala1889= (c.5667C>T)?

CHD5 p.Ala1889= (c.5667C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CHD5 p.Ala1889= (c.5667C>T) in the general population?

CHD5 p.Ala1889= (c.5667C>T) is ultra-rare (popmax 0.0446%, eas) (gnomAD).

CHD5 p.Ala1889=

c.5667C>T · rs768719057 · VCV3144160

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0446%, eas)

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 -8.2	GERP -4
Overall
CADD	4.557	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0446% East Asian · 20/44,834 alleles

Filtering AF 0.0295% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0246%

Overall 0.00236% 38/1,611,524 alleles · ultra-rare exomes 36/1,459,494 · genomes 2/152,030 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0446%	2,242
Admixed American	0.00668%	14,970
Remaining individualsnot grpmax-eligible	0.00481%	20,797
European (non-Finnish)	0.000932%	107,240

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: CHD5
Protein: p.Ala1889=
Coding: c.5667C>T
MANE Select: NM_015557
dbSNP: rs768719057
Type: single nucleotide variant
Location: chr1:6106691 (GRCh38)
Structure: AlphaFold pLDDT 78.15 · 4 PDB

Full CHD5 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

Similar variants

CHD5 p.Ala1435Thr Uncertain significance ★★ ⚠ same condition
CHD5 p.Ala1446Ser Uncertain significance ★★ ⚠ same condition
CHD5 p.Ala215Val Uncertain significance ★★ same condition
CHD5 p.Arg1337Cys Uncertain significance ★★ same condition
CHD5 p.Asn21Ser Uncertain significance ★★ ⚠ same condition
CHD5 p.Asp414Asn Uncertain significance ★★ same condition
CHD5 p.Gln979His Uncertain significance ★★ ⚠ same condition
CHD5 p.Glu1302Val Uncertain significance ★★ ⚠ 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/chd5-p-ala1889 (accessed [today's date]).

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