EMP2 c.169+9G>C
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 30.1%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -2.9, phastCons 0.002 |
| Overall | ||
| CADD | 9.088 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
30.1%
African / African-American · 22,570/74,992 alleles
Filtering AF
29.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 29.6%
Overall
6.75%
108,919/1,613,728 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 30.1% | 3 |
| South Asian | 12.7% | 8 |
| East Asian | 11.3% | 9 |
| Remaining individualsnot grpmax-eligible | 7.77% | 13 |
| Middle Eastern | 7.34% | 14 |
| Finnishnot grpmax-eligible | 7.1% | 14 |
| Ashkenazi Jewishnot grpmax-eligible | 6.86% | 15 |
| Amishnot grpmax-eligible | 6.72% | 15 |
| European (non-Finnish) | 4.68% | 21 |
| Admixed American | 4.13% | 24 |
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.169+9G>C
- MANE Select
- NM_001424
- dbSNP
- rs2089185
- Type
- single nucleotide variant
- Location
- chr16:10543561 (GRCh38)
- Gene constraint
- LOEUF 1.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.89
Similar variants
- EMP2 p.Ala63Val Uncertain significance ★★ ⚠ same type
- EMP2 p.Ala78Thr Uncertain significance ★★ ⚠ same type
- EMP2 p.Arg120His Uncertain significance ★★ ⚠ same type
- EMP2 p.Arg166His Uncertain significance ★★ ⚠ same type
- EMP2 p.Glu121Lys Uncertain significance ★★ ⚠ same type
- EMP2 p.Ile69Met Uncertain significance ★★ ⚠ same type
- EMP2 p.Thr43Ile Uncertain significance ★★ ⚠ same type
- EMP2 p.Tyr143His 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/emp2-c-169-plus-9g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown