EML6 p.Ile220=
c.660C>T · rs116185852 · VCV775716
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.63%, 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 1.4 | GERP 0.4, phastCons 1 |
| Overall | ||
| CADD | 8.992 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.63%
African / African-American · 1,193/73,138 alleles
Filtering AF
1.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.52%
Overall
0.0822%
1,276/1,551,664 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.63% | 61 |
| Remaining individualsnot grpmax-eligible | 0.0782% | 1,279 |
| Admixed American | 0.0627% | 1,594 |
| South Asian | 0.00119% | 84,054 |
| European (non-Finnish) | 0.000262% | 382,316 |
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
- EML6
- Protein
- p.Ile220=
- Coding
- c.660C>T
- MANE Select
- NM_001039753
- dbSNP
- rs116185852
- Type
- single nucleotide variant
- Location
- chr2:54827700 (GRCh38)
- Gene constraint
- LOEUF 0.726 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.42
Similar variants
- EML6 p.Arg475Gln Uncertain significance ★★ ⚠ same type
- EML6 p.Gly1925Ser Uncertain significance ★★ ⚠ same type
- EML6 p.Thr199Ser Uncertain significance ★★ ⚠ same type
- EML6 p.Glu1412= Benign ★★ same type
- EML6 p.His1237= Benign ★★ same type
- EML6 p.His662= Benign ★★ same type
- EML6 p.Ala1014Thr Uncertain significance ★ ⚠ same type
- EML6 p.Ala1056Thr 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/eml6-p-ile220 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown