ELF3 p.Asn104=
c.312T>C · rs115158470 · VCV775154
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.82%, 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 0.47 | GERP 0.045, phastCons 0.054 |
| Overall | ||
| CADD | 7.064 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.82%
African / African-American · 1,363/75,052 alleles
Filtering AF
1.74%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.7%
Overall
0.13%
2,094/1,614,126 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.82% | 55 |
| Middle Eastern | 0.316% | 317 |
| Remaining individualsnot grpmax-eligible | 0.229% | 437 |
| Admixed American | 0.21% | 476 |
| Ashkenazi Jewishnot grpmax-eligible | 0.186% | 538 |
| European (non-Finnish) | 0.0323% | 3,097 |
| South Asian | 0.00549% | 18,216 |
| East Asian | 0.00223% | 44,874 |
| Finnishnot grpmax-eligible | 0.00156% | 64,036 |
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
- ELF3
- Protein
- p.Asn104=
- Coding
- c.312T>C
- MANE Select
- NM_004433
- dbSNP
- rs115158470
- Type
- single nucleotide variant
- Location
- chr1:202012105 (GRCh38)
- Gene constraint
- LOEUF 0.678 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.32 · 1 PDB
- Residue 104
- the pnt domain; an α-helix
Similar variants
- ELF3 p.Arg205Trp Uncertain significance ★ ⚠ same type
- ELF3 p.Arg233Cys Uncertain significance ★ ⚠ same type
- ELF3 p.Arg307His Uncertain significance ★ ⚠ same type
- ELF3 p.Arg370Gln Uncertain significance ★ ⚠ same type
- ELF3 p.Arg370Trp Uncertain significance ★ ⚠ same type
- ELF3 p.Asp220Tyr Uncertain significance ★ ⚠ same type
- ELF3 p.Asp234Asn Uncertain significance ★ ⚠ same type
- ELF3 p.Asp96Glu 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/elf3-p-asn104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown