E2F7 p.Asp478=
c.1434C>T · rs61758459 · VCV708022
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.23%, nfe)
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 1 | GERP 2, phastCons 0.45 |
| Overall | ||
| CADD | 3.842 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.23%
European (non-Finnish) · 14,398/1,166,174 alleles
Filtering AF
1.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.21%
Overall
1.06%
16,910/1,590,012 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.23% | 81 |
| Finnishnot grpmax-eligible | 1.23% | 82 |
| Remaining individualsnot grpmax-eligible | 0.954% | 105 |
| South Asian | 0.662% | 151 |
| Ashkenazi Jewishnot grpmax-eligible | 0.54% | 185 |
| Admixed American | 0.475% | 210 |
| Middle Eastern | 0.219% | 456 |
| African / African-American | 0.175% | 572 |
| East Asian | 0.00225% | 44,470 |
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.Asp478=
- Coding
- c.1434C>T
- MANE Select
- NM_203394
- dbSNP
- rs61758459
- Type
- single nucleotide variant
- Location
- chr12:77030281 (GRCh38)
- Gene constraint
- LOEUF 0.58 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 51.31
Similar variants
- E2F7 p.Arg645Thr 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
- E2F7 p.Ala406Ser Uncertain significance ★ ⚠ same type
- E2F7 p.Ala466Val 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-asp478 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown