Is EED c.552+155G>A pathogenic?

EED c.552+155G>A is classified Benign in EED (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-05-11). Common (popmax 41.3%, nfe) — too common for a highly-penetrant pathogenic allele.

EED c.552+155G>A

Q: How common is EED c.552+155G>A in the general population?

EED c.552+155G>A is common (popmax 41.3%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs10792842 · VCV1279124

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 41.3%, 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 +155	deep intronic (+155 nt into the intron)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2	GERP -4.1
Non-coding constraint	Z -0.11	1 kb window · o/e 1.01 · regional · uncalibrated
Overall
CADD	0.356	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 41.3% European (non-Finnish) · 28,071/67,952 alleles

Filtering AF 40.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 40.7%

Overall 33.3% 50,618/152,076 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	51.6%	2
Finnishnot grpmax-eligible	42.5%	2
European (non-Finnish)grpmax	41.3%	2
South Asian	40.6%	2
East Asian	34.4%	3
Remaining individualsnot grpmax-eligible	34.3%	3
Middle Eastern	31.6%	3
Admixed American	30.4%	3
Ashkenazi Jewishnot grpmax-eligible	29.6%	3
African / African-American	17.8%	6

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.552+155G>A
MANE Select: NM_003797
dbSNP: rs10792842
Type: single nucleotide variant
Location: chr11:86256667 (GRCh38)
Gene constraint: LOEUF 0.41 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 87.21 · 81 PDB

Full EED gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EED p.Asn194Ser Pathogenic/Likely pathogenic ★★ same type
EED p.Asp237Gly Likely pathogenic ★★ same type
EED p.Ala17Val Uncertain significance ★★ ⚠ same type
EED p.Arg4Met Uncertain significance ★★ ⚠ same type
EED p.Lys83Ile Uncertain significance ★★ ⚠ same type
EED c.267+20C>G Benign/Likely benign ★★ same type
EED c.268-43G>A Benign ★★ same type
EED c.361-19G>A Likely 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-552-plus-155g-a (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown