ECI1 p.Arg92=
c.276C>T · VCV4684062
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.152%, 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 -8 | GERP -4.2 |
| Overall | ||
| CADD | 0.259 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.152%
European (non-Finnish) · 1,790/1,180,012 alleles
Filtering AF
0.146%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.143%
Overall
0.119%
1,912/1,613,134 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.152% | 659 |
| Remaining individualsnot grpmax-eligible | 0.0753% | 1,328 |
| Finnishnot grpmax-eligible | 0.0628% | 1,592 |
| Middle Eastern | 0.0181% | 5,532 |
| African / African-American | 0.016% | 6,252 |
| South Asian | 0.0143% | 7,003 |
| Admixed American | 0.0117% | 8,573 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| East Asian | 0.00223% | 44,890 |
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
- ECI1
- Protein
- p.Arg92=
- Coding
- c.276C>T
- MANE Select
- NM_001919
- Type
- single nucleotide variant
- Location
- chr16:2246877 (GRCh38)
- Gene constraint
- LOEUF 1.485 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.43 · 1 PDB
Similar variants
- ECI1 p.Arg92Cys Uncertain significance ★ ⚠ same residue
- ECI1 p.Arg92Pro Uncertain significance ★ ⚠ same residue
- ECI1 p.Thr76Met Benign ★★ same type
- ECI1 p.Ala119Thr Uncertain significance ★ ⚠ same type
- ECI1 p.Ala185Ser Uncertain significance ★ ⚠ same type
- ECI1 p.Ala19Ser Uncertain significance ★ ⚠ same type
- ECI1 p.Ala201Val Uncertain significance ★ ⚠ same type
- ECI1 p.Ala202Val Uncertain significance ★ 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/eci1-p-arg92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown