ELF4 p.Asn17=
c.51C>T · VCV3905695
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00654%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.5 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 12.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00654%
Admixed American · 3/45,863 alleles
Filtering AF
0.00174%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000881%
Overall
0.000496%
6/1,210,826 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00654% | 15,288 |
| East Asian | 0.00296% | 33,792 |
| African / African-American | 0.00174% | 57,501 |
| European (non-Finnish) | 0.000112% | 895,367 |
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
- ELF4
- Protein
- p.Asn17=
- Coding
- c.51C>T
- MANE Select
- NM_001421
- Type
- single nucleotide variant
- Location
- chrX:130081280 (GRCh38)
- Structure
- AlphaFold pLDDT 49.77
Similar variants
- ELF4 p.Gly206Asp Uncertain significance ★★ ⚠ same type
- ELF4 p.Ser413Leu Uncertain significance ★★ ⚠ same type
- ELF4 p.Ala147Val Benign/Likely benign ★★ same type
- ELF4 p.Arg604Cys Benign ★★ same type
- ELF4 p.Ser369= Benign ★★ same type
- ELF4 p.Thr503= Benign ★★ same type
- ELF4 p.Arg185Ter Likely pathogenic ★ same type
- ELF4 p.Arg234Ter Pathogenic ★ 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/elf4-p-asn17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown