Is E2F7 p.Gln892= (c.2676G>A) pathogenic?

E2F7 p.Gln892= (c.2676G>A) is classified Benign in E2F7 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-04-12). Rare (popmax 0.223%, amr).

How common is E2F7 p.Gln892= (c.2676G>A) in the general population?

E2F7 p.Gln892= (c.2676G>A) is rare (popmax 0.223%, amr) (gnomAD).

E2F7 p.Gln892=

c.2676G>A · rs370128394 · VCV726441

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.223%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.34	GERP -0.61
Overall
CADD	5.999	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.223% Admixed American · 134/59,990 alleles

Filtering AF 0.193% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.181%

Overall 0.0083% 134/1,613,932 alleles · rare

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: E2F7
Protein: p.Gln892=
Coding: c.2676G>A
MANE Select: NM_203394
dbSNP: rs370128394
Type: single nucleotide variant
Location: chr12:77024075 (GRCh38)
Gene constraint: LOEUF 0.58 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 51.31
Residue 892: the 'disordered' region

Full E2F7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

E2F7 p.Gln892His Uncertain significance ★ ⚠ same residue
E2F7 p.Arg645Thr Benign ★★ same type
E2F7 p.Asp478= Benign ★★ same type
E2F7 p.Pro431= Benign ★★ same type
E2F7 p.Pro857= Benign ★★ same type
E2F7 p.Tyr843= Benign ★★ same type
E2F7 p.Ala117Thr Uncertain significance ★ ⚠ same type
E2F7 p.Ala131Thr Uncertain significance ★ ⚠ 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/e2f7-p-gln892 (accessed [today's date]).

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