ERCC8 c.550+3A>C
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | Δ0.76 | donor loss, 3 bp away · masked 0 · deltas |
| Pangolin | Δ0.61 | loss · gain 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 1.9, phastCons 1 |
| Non-coding constraint | Z 0.53 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 18.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ERCC8
- Coding
- c.550+3A>C
- MANE Select
- NM_000082
- Type
- single nucleotide variant
- Location
- chr5:60903645 (GRCh38)
- Gene constraint
- LOEUF 1.608 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.72 · 16 PDB
Similar variants
- ERCC8 c.1041+1G>T Pathogenic/Likely pathogenic ★★ same type
- ERCC8 c.1042-2A>G Pathogenic/Likely pathogenic ★★ same type
- ERCC8 c.173+1119G>C Pathogenic/Likely pathogenic ★★ same type
- ERCC8 c.173+1G>A Pathogenic/Likely pathogenic ★★ same type
- ERCC8 c.275+1G>A Pathogenic ★★ same type
- ERCC8 c.276-1G>A Likely pathogenic ★★ same type
- ERCC8 c.399+1G>A Likely pathogenic ★★ same type
- ERCC8 c.551-1G>A 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/ercc8-c-550-plus-3a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown