NBEA p.Arg1980=
c.5940T>C · rs111297138 · VCV714577
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.34%, 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 -4.8 | GERP -4.6 |
| Overall | ||
| CADD | 3.036 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.34%
African / African-American · 1,750/74,814 alleles
Filtering AF
2.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.21%
Overall
0.124%
1,988/1,608,462 alleles · low-frequency
exomes 1,016/1,456,210 · genomes 972/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.34% | 43 |
| Middle Eastern | 0.183% | 548 |
| Remaining individualsnot grpmax-eligible | 0.172% | 582 |
| Admixed American | 0.144% | 693 |
| South Asian | 0.0155% | 6,447 |
| European (non-Finnish) | 0.0017% | 58,833 |
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
- NBEA
- Protein
- p.Arg1980=
- Coding
- c.5940T>C
- MANE Select
- NM_001385012
- dbSNP
- rs111297138
- Type
- single nucleotide variant
- Location
- chr13:35349144 (GRCh38)
- Gene constraint
- LOEUF 0.137 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 1980
- a UniProt-annotated variant site (in nedege)
Similar variants
- NBEA p.Arg1980Cys Uncertain significance ★ same residue
- NBEA p.Arg1299Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Arg145Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Arg2213Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Arg2866Ter Pathogenic ★★ same type
- NBEA p.Arg696Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Asp319Tyr Likely pathogenic ★★ same type
- NBEA c.4242+5G>A 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/nbea-p-arg1980 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown