EED c.267+141del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 37.1%, nfe) — 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 +141 | deep intronic (+141 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.76 | GERP -2 |
| Non-coding constraint | Z 0.58 | 1 kb window · o/e 0.96 · regional · uncalibrated |
| Overall | ||
| CADD | 1.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
37.1%
European (non-Finnish) · 243,377/656,104 alleles
Filtering AF
37%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 36.9%
Overall
35.8%
309,809/866,284 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 37.1% | 3 |
| Middle Eastern | 36.5% | 3 |
| Remaining individualsnot grpmax-eligible | 36.2% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 35.5% | 3 |
| Finnishnot grpmax-eligible | 33.9% | 3 |
| African / African-American | 32% | 3 |
| Admixed American | 29.2% | 3 |
| South Asian | 28% | 4 |
| East Asian | 24.4% | 4 |
| Amishnot grpmax-eligible | 24.2% | 4 |
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
- EED
- Coding
- c.267+141del
- MANE Select
- NM_003797
- dbSNP
- rs35137499
- Type
- Deletion
- Location
- chr11:86250579 (GRCh38)
- Gene constraint
- LOEUF 0.41 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.21 · 81 PDB
Similar variants
- EED p.Lys89fs Uncertain significance ★★ same type
- EED c.1199+8_1199+11del Benign/Likely benign ★★ same type
- EED c.268-7_268-3del Likely benign ★ same type
- EED c.553-157del Benign ★ 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/eed-c-267-plus-141del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown