EMP2 c.*164del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 80.9%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Overall | ||
| CADD | 0.909 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (T)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
80.9%
African / African-American · 24,004/29,670 alleles
Filtering AF
80%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 79.7%
Overall
59%
119,021/201,866 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 80.9% | 1 |
| South Asian | 79.3% | 1 |
| East Asian | 76.4% | 1 |
| Amishnot grpmax-eligible | 74.8% | 1 |
| Admixed American | 64.4% | 2 |
| Finnishnot grpmax-eligible | 61.5% | 2 |
| European (non-Finnish) | 52.6% | 2 |
| Remaining individualsnot grpmax-eligible | 49.6% | 2 |
| Middle Eastern | 47.1% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 43.4% | 2 |
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
- EMP2
- Coding
- c.*164del
- MANE Select
- NM_001424
- dbSNP
- rs35927182
- Type
- Deletion
- Location
- chr16:10532741 (GRCh38)
- Gene constraint
- LOEUF 1.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.89
Similar variants
- EMP2 p.Trp29_Val30delinsTer Likely pathogenic ★ 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/emp2-c-star-164del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown