EFCAB8 p.Ser183=
c.549G>A · rs139861538 · VCV2652259
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.03%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.043 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -2.8 |
| Overall | ||
| CADD | 1.332 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.03%
European (non-Finnish) · 11,818/1,147,002 alleles
Filtering AF
1.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.01%
Overall
0.896%
13,910/1,551,758 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.03% | 97 |
| Remaining individualsnot grpmax-eligible | 1.02% | 98 |
| South Asian | 0.796% | 126 |
| Finnishnot grpmax-eligible | 0.591% | 169 |
| Middle Eastern | 0.501% | 200 |
| Admixed American | 0.461% | 217 |
| Ashkenazi Jewishnot grpmax-eligible | 0.255% | 392 |
| African / African-American | 0.157% | 636 |
| East Asian | 0.00733% | 13,638 |
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
- EFCAB8
- Protein
- p.Ser183=
- Coding
- c.549G>A
- MANE Select
- NM_001143967
- dbSNP
- rs139861538
- Type
- single nucleotide variant
- Location
- chr20:32885622 (GRCh38)
- Gene constraint
- LOEUF 0.946 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.52
Similar variants
- EFCAB8 p.Leu175= 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/efcab8-p-ser183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown