EED c.726+19G>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0162%, afr)
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 4.8 | GERP 2.1, phastCons 1 |
| Non-coding constraint | Z -0.97 | 1 kb window · o/e 1.07 · regional · uncalibrated |
| Overall | ||
| CADD | 12.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0162%
African / African-American · 12/74,160 alleles
Filtering AF
0.0093%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00728%
Overall
0.000885%
14/1,581,816 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0162% | 6,180 |
| Admixed American | 0.00167% | 59,876 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,386 |
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.726+19G>A
- MANE Select
- NM_003797
- dbSNP
- rs763050365
- Type
- single nucleotide variant
- Location
- chr11:86264282 (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-726-plus-19g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown