Is CHD5 p.Asp1690= (c.5070C>T) pathogenic?

CHD5 p.Asp1690= (c.5070C>T) is classified Likely benign in CHD5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-07). Rare (popmax 0.16%, afr); Associated with Inborn genetic diseases.

What condition is associated with CHD5 p.Asp1690= (c.5070C>T)?

CHD5 p.Asp1690= (c.5070C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CHD5 p.Asp1690= (c.5070C>T) in the general population?

CHD5 p.Asp1690= (c.5070C>T) is rare (popmax 0.16%, afr) (gnomAD).

CHD5 p.Asp1690=

c.5070C>T · VCV3832818

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.16%, 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 -0.68	GERP -2.9, phastCons 0.012
Overall
CADD	7.654	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.16% African / African-American · 120/74,924 alleles

Filtering AF 0.137% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.128%

Overall 0.0109% 176/1,613,884 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.16%	624
East Asian	0.0201%	4,985
Remaining individualsnot grpmax-eligible	0.0096%	10,416
Admixed American	0.00667%	14,998
European (non-Finnish)	0.00297%	33,714
South Asian	0.0022%	45,533

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.Asp1690=
Coding: c.5070C>T
MANE Select: NM_004627 · reported on NM_015557
Type: single nucleotide variant
Location: chr1:6112210 (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-asp1690 (accessed [today's date]).

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