EED c.966+19A>C
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0628%, nfe)
Conditions
1
Cohen-Gibson syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 2.4, phastCons 1 |
| Non-coding constraint | Z 2.15 | 1 kb window · o/e 0.81 · regional · uncalibrated |
| Overall | ||
| CADD | 20.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0628%
European (non-Finnish) · 652/1,038,406 alleles
Filtering AF
0.0587%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0572%
Overall
0.0459%
665/1,449,942 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0628% | 1,593 |
| Remaining individualsnot grpmax-eligible | 0.0157% | 6,361 |
| African / African-American | 0.00434% | 23,057 |
| Admixed American | 0.00175% | 57,090 |
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.966+19A>C
- MANE Select
- NM_003797
- dbSNP
- rs201522182
- Type
- single nucleotide variant
- Location
- chr11:86268580 (GRCh38)
- Gene constraint
- LOEUF 0.41 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.21 · 81 PDB
Similar variants
- EED p.Asn194Ser Pathogenic/Likely pathogenic ★★ same condition
- EED p.Asp237Gly Likely pathogenic ★★ same condition
- EED p.Ala17Val Uncertain significance ★★ ⚠ same condition
- EED p.Arg4Met Uncertain significance ★★ ⚠ same condition
- EED p.Lys83Ile Uncertain significance ★★ ⚠ same condition
- EED c.267+20C>G Benign/Likely benign ★★ same condition
- EED c.361-19G>A Likely benign ★★ same condition
- EED c.727-8G>A Benign ★★ same condition
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-966-plus-19a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown