ELFN1 p.Ser823=
c.2469G>A · rs114713154 · VCV789754
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 4.16%, 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 -13 | GERP -2.3 |
| Overall | ||
| CADD | 4.369 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.16%
African / African-American · 2,987/71,844 alleles
Filtering AF
4.03%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.98%
Overall
0.251%
3,793/1,511,768 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.16% | 24 |
| Admixed American | 0.39% | 256 |
| Remaining individualsnot grpmax-eligible | 0.373% | 268 |
| Middle Eastern | 0.273% | 367 |
| European (non-Finnish) | 0.0333% | 3,004 |
| Finnishnot grpmax-eligible | 0.017% | 5,868 |
| South Asian | 0.00383% | 26,141 |
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
- ELFN1
- Protein
- p.Ser823=
- Coding
- c.2469G>A
- MANE Select
- NM_001128636
- dbSNP
- rs114713154
- Type
- single nucleotide variant
- Location
- chr7:1747065 (GRCh38)
- Gene constraint
- LOEUF 1.841 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.62 · 5 PDB
Similar variants
- ELFN1 p.Ala14= Benign/Likely benign ★★ same type
- ELFN1 p.Ala796= Benign/Likely benign ★★ same type
- ELFN1 p.Asp618= Likely benign ★★ same type
- ELFN1 p.Cys196= Likely benign ★★ same type
- ELFN1 p.Glu258= Benign/Likely benign ★★ same type
- ELFN1 p.Gly228= Benign/Likely benign ★★ same type
- ELFN1 p.His20= Benign/Likely benign ★★ same type
- ELFN1 p.Pro614= Benign/Likely benign ★★ 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/elfn1-p-ser823 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown