ERCC4 c.1102+307G>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 51.5%, afr) — 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 | ||
| Splice region | donor +307 | deep intronic (+307 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP -1.9 |
| Non-coding constraint | Z 0.85 | 1 kb window · o/e 0.92 · regional · uncalibrated |
| Overall | ||
| CADD | 0.026 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
51.5%
African / African-American · 25,388/49,310 alleles
Filtering AF
51%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 50.7%
Overall
10.9%
50,024/460,612 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 51.5% | 2 |
| Amishnot grpmax-eligible | 12.2% | 8 |
| Admixed American | 11.4% | 9 |
| Middle Eastern | 9.88% | 10 |
| Remaining individualsnot grpmax-eligible | 9.74% | 10 |
| Ashkenazi Jewishnot grpmax-eligible | 9.42% | 11 |
| Finnishnot grpmax-eligible | 7.12% | 14 |
| European (non-Finnish) | 5.86% | 17 |
| South Asian | 2.45% | 41 |
| East Asian | 0.124% | 810 |
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
- ERCC4
- Coding
- c.1102+307G>A
- MANE Select
- NM_005236
- dbSNP
- rs3136124
- Type
- single nucleotide variant
- Location
- chr16:13932592 (GRCh38)
- Gene constraint
- LOEUF 0.984 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.60 · 13 PDB
Similar variants
- ERCC4 c.1102+1G>T Likely pathogenic ★★ same type
- ERCC4 c.793-2A>G Pathogenic ★★ same type
- ERCC4 p.Arg20Ter Pathogenic ★★ same type
- ERCC4 p.Arg589Trp Pathogenic/Likely pathogenic ★★ same type
- ERCC4 p.Arg689Ser Likely pathogenic ★★ same type
- ERCC4 p.Arg772Ter Pathogenic/Likely pathogenic ★★ same type
- ERCC4 p.Cys236Arg Pathogenic/Likely pathogenic ★★ same type
- ERCC4 p.Cys723Ter Pathogenic/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/ercc4-c-1102-plus-307g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown