ELFN1 p.Pro675=
c.2025C>T · rs747238069 · VCV738772
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.241%, 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 -7.8 | GERP -2.4 |
| Overall | ||
| CADD | 0.507 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.241%
South Asian · 141/58,566 alleles
Filtering AF
0.208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.196%
Overall
0.0151%
204/1,349,908 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.241% | 415 |
| Remaining individualsnot grpmax-eligible | 0.0177% | 5,637 |
| European (non-Finnish) | 0.00512% | 19,549 |
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.Pro675=
- Coding
- c.2025C>T
- MANE Select
- NM_001128636
- dbSNP
- rs747238069
- Type
- single nucleotide variant
- Location
- chr7:1746621 (GRCh38)
- Gene constraint
- LOEUF 1.841 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.62 · 5 PDB
Similar variants
- ELFN1 p.Pro675Ala Uncertain significance ★ ⚠ same residue
- ELFN1 p.Pro675Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro675 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown