Is CHD5 p.Asp1909fs (c.5725del) pathogenic?

CHD5 p.Asp1909fs (c.5725del) is classified Uncertain significance in CHD5 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-01). No allele count reported in gnomAD v4.1 (AN 1,581,374).

How common is CHD5 p.Asp1909fs (c.5725del) in the general population?

CHD5 p.Asp1909fs (c.5725del) is no allele count reported in gnomAD v4.1 (AN 1,581,374) (gnomAD).

CHD5 p.Asp1909fs

c.5725del · rs2100825800 · VCV1675338

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,581,374)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.8	GERP -0.08, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,581,374). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHD5
Protein: p.Asp1909fs
Coding: c.5725del
MANE Select: NM_015557
dbSNP: rs2100825800
Type: Deletion
Location: chr1:6106633 (GRCh38)
Structure: AlphaFold pLDDT 78.15 · 4 PDB

Full CHD5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CHD5 p.Ala1853fs Likely pathogenic ★ same type
CHD5 p.Asn1229fs Pathogenic ★ same type
CHD5 p.Ile839fs Likely pathogenic ★ same type
CHD5 p.Leu1019fs Pathogenic ★ same type
CHD5 p.Leu574fs Pathogenic ★ same type
CHD5 p.Val1453fs Likely pathogenic ★ same type
CHD5 c.1161+8_1161+38del Uncertain significance ★ same type
CHD5 c.4394+5del Uncertain significance ★ same type

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-asp1909fs (accessed [today's date]).

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