ELFN1 p.Ser411=
c.1233C>T · rs372994834 · VCV709257
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.971%, 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 1.6 | GERP 0.37, phastCons 1 |
| Overall | ||
| CADD | 8.582 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.971%
African / African-American · 719/74,018 alleles
Filtering AF
0.913%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.889%
Overall
0.0521%
822/1,577,060 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.971% | 103 |
| Remaining individualsnot grpmax-eligible | 0.101% | 988 |
| Admixed American | 0.0442% | 2,262 |
| Middle Eastern | 0.0331% | 3,018 |
| South Asian | 0.00231% | 43,206 |
| Finnishnot grpmax-eligible | 0.0017% | 58,878 |
| European (non-Finnish) | 0.00103% | 96,973 |
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.Ser411=
- Coding
- c.1233C>T
- MANE Select
- NM_001128636
- dbSNP
- rs372994834
- Type
- single nucleotide variant
- Location
- chr7:1745829 (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-ser411 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown