ERCC6 c.*232del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 27.5%, sas) — too common for a highly-penetrant pathogenic allele
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 -0.34 | GERP -2.7, phastCons 0.001 |
| Non-coding constraint | Z 0.51 | 1 kb window · o/e 0.96 · regional · uncalibrated |
| Overall | ||
| CADD | 0.161 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
27.5%
South Asian · 8,278/30,084 alleles
Filtering AF
27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 26.8%
Overall
18.6%
73,353/393,870 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 27.5% | 4 |
| Remaining individualsnot grpmax-eligible | 24.6% | 4 |
| East Asian | 22.5% | 4 |
| Middle Eastern | 22.5% | 4 |
| European (non-Finnish) | 20.1% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 19.7% | 5 |
| Finnishnot grpmax-eligible | 17.2% | 6 |
| Admixed American | 13.6% | 7 |
| African / African-American | 4.68% | 21 |
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
- ERCC6
- Coding
- c.*232del
- MANE Select
- NM_000124
- dbSNP
- rs74561842
- Type
- Deletion
- Location
- chr10:49458583 (GRCh38)
- Gene constraint
- LOEUF 0.803 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.12 · 12 PDB
Similar variants
- ERCC6 p.Ala1167fs Pathogenic/Likely pathogenic ★★ same type
- ERCC6 p.Arg1318fs Pathogenic/Likely pathogenic ★★ same type
- ERCC6 p.Gly270fs Pathogenic/Likely pathogenic ★★ same type
- ERCC6 p.Gly347fs Pathogenic/Likely pathogenic ★★ same type
- ERCC6 p.Ile931fs Pathogenic/Likely pathogenic ★★ same type
- ERCC6 p.Lys506fs Pathogenic/Likely pathogenic ★★ same type
- ERCC6 p.Ser49fs Pathogenic ★★ same type
- ERCC6 p.Tyr1179fs 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/ercc6-c-star-232del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown