ERCC3 c.822+17del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +17 | near-intronic (+17 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.7 | GERP -2.8, phastCons 0.092 |
| Non-coding constraint | Z 1.91 | 1 kb window · o/e 0.88 · regional · uncalibrated |
| Overall | ||
| CADD | 1.251 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,002 alleles
Filtering AF
0.00088%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000719%
Overall
0.00118%
19/1,610,066 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,002 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,332 |
| European (non-Finnish) | 0.00144% | 69,218 |
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
- ERCC3
- Coding
- c.822+17del
- MANE Select
- NM_000122
- dbSNP
- rs1351312042
- Type
- Deletion
- Location
- chr2:127289320 (GRCh38)
- Gene constraint
- LOEUF 0.797 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.34 · 56 PDB
Similar variants
- ERCC3 p.Gln586fs Pathogenic/Likely pathogenic ★★ same type
- ERCC3 p.Tyr579fs Pathogenic/Likely pathogenic ★★ same type
- ERCC3 p.Val193fs Pathogenic/Likely pathogenic ★★ same type
- ERCC3 p.Ala562fs Pathogenic ★ same type
- ERCC3 p.Asp237fs Likely pathogenic ★ same type
- ERCC3 p.Cys342fs Pathogenic ★ same type
- ERCC3 p.Glu288fs Pathogenic ★ same type
- ERCC3 p.Glu372fs Likely pathogenic ★ 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/ercc3-c-822-plus-17del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown