ELFN1 p.Ile99=
c.297C>T · rs202117598 · VCV710659
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.55%, sas)
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 -7.6 | GERP -3.1 |
| Overall | ||
| CADD | 7.374 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.55%
South Asian · 1,307/84,564 alleles
Filtering AF
1.48%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.45%
Overall
0.22%
3,426/1,559,432 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.55% | 65 |
| Ashkenazi Jewishnot grpmax-eligible | 0.587% | 170 |
| Middle Eastern | 0.583% | 171 |
| Remaining individualsnot grpmax-eligible | 0.241% | 414 |
| European (non-Finnish) | 0.144% | 693 |
| Finnishnot grpmax-eligible | 0.0964% | 1,037 |
| Admixed American | 0.0367% | 2,726 |
| East Asian | 0.0286% | 3,493 |
| African / African-American | 0.0258% | 3,875 |
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.Ile99=
- Coding
- c.297C>T
- MANE Select
- NM_001128636
- dbSNP
- rs202117598
- Type
- single nucleotide variant
- Location
- chr7:1744893 (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-ile99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown