ELFN1 p.Ser296=
c.888C>T · rs202182712 · VCV716639
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.103%, nfe)
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 -20 | GERP -3.3 |
| Overall | ||
| CADD | 0.028 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.103%
European (non-Finnish) · 1,179/1,146,748 alleles
Filtering AF
0.0979%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.096%
Overall
0.0845%
1,304/1,542,932 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.103% | 973 |
| Remaining individualsnot grpmax-eligible | 0.0766% | 1,305 |
| Finnishnot grpmax-eligible | 0.0621% | 1,610 |
| African / African-American | 0.0355% | 2,814 |
| Admixed American | 0.0235% | 4,249 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0105% | 9,541 |
| South Asian | 0.00714% | 14,002 |
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.Ser296=
- Coding
- c.888C>T
- MANE Select
- NM_001128636
- dbSNP
- rs202182712
- Type
- single nucleotide variant
- Location
- chr7:1745484 (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-ser296 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown