CHD4 c.4516del
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.9, phastCons 1 |
| Non-coding constraint | Z 1.56 | 1 kb window · o/e 0.89 · regional · uncalibrated |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. 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
- CHD4
- Coding
- c.4516del
- MANE Select
- NM_001273
- dbSNP
- rs2540380595
- Type
- Deletion
- Location
- chr12:6581814 (GRCh38)
- Gene constraint
- LOEUF 0.192 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.41 · 12 PDB
Similar variants
- CHD4 p.Lys354del Uncertain significance ★★ same type
- CHD4 c.2514+8_2514+9del Likely benign ★★ same type
- CHD4 c.3340+10_3340+12del Likely benign ★★ same type
- CHD4 p.Leu1219fs Pathogenic ★ same type
- CHD4 p.Val1298fs Likely pathogenic ★ same type
- CHD4 p.Val888fs Likely pathogenic ★ same type
- CHD4 c.4146_4147+10del Uncertain significance ★ same type
- CHD4 p.Arg80fs 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/chd4-c-4516del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown