ELF1 p.Leu614=
c.1842G>A · rs115657038 · VCV768611
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.64%, afr)
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 1.2 | GERP 0.97, phastCons 1 |
| Overall | ||
| CADD | 5.678 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.64%
African / African-American · 1,977/74,910 alleles
Filtering AF
2.54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.5%
Overall
0.138%
2,226/1,612,984 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.64% | 38 |
| Remaining individualsnot grpmax-eligible | 0.215% | 466 |
| Admixed American | 0.145% | 688 |
| Middle Eastern | 0.0826% | 1,211 |
| South Asian | 0.0055% | 18,178 |
| East Asian | 0.00223% | 44,878 |
| European (non-Finnish) | 0.00144% | 69,377 |
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
- ELF1
- Protein
- p.Leu614=
- Coding
- c.1842G>A
- MANE Select
- NM_032377 · reported on NM_172373
- dbSNP
- rs115657038
- Type
- single nucleotide variant
- Location
- chr13:40933443 (GRCh38)
- Structure
- AlphaFold pLDDT 85.98 · 7 PDB
Similar variants
- ELF1 p.Pro364= Benign ★★ same type
- ELF1 p.Ala29Thr Uncertain significance ★ ⚠ same type
- ELF1 p.Ala353Ser Uncertain significance ★ ⚠ same type
- ELF1 p.Ala459Val Uncertain significance ★ ⚠ same type
- ELF1 p.Arg323Thr Uncertain significance ★ ⚠ same type
- ELF1 p.Arg328Gln Uncertain significance ★ ⚠ same type
- ELF1 p.Arg330Lys Uncertain significance ★ ⚠ same type
- ELF1 p.Arg369Lys 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/elf1-p-leu614 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown