NFRKB p.Val504=
c.1512A>G · rs200767687 · VCV3198265
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.924%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.61 | acceptor loss, 3 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.4 | GERP 0.76, phastCons 1 |
| Overall | ||
| CADD | 14.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.924%
Middle Eastern · 56/6,062 alleles
Filtering AF
0.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.661%
Overall
0.00818%
132/1,614,146 alleles · rare
exomes 126/1,461,864 · genomes 6/152,282 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.924% | 108 |
| African / African-American | 0.00933% | 10,720 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,501 |
| Admixed American | 0.00667% | 15,003 |
| European (non-Finnish) | 0.00466% | 21,455 |
| South Asian | 0.00329% | 30,363 |
| Finnishnot grpmax-eligible | 0.00312% | 32,016 |
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
- NFRKB
- Protein
- p.Val504=
- Coding
- c.1512A>G
- MANE Select
- NM_001143835
- dbSNP
- rs200767687
- Type
- single nucleotide variant
- Location
- chr11:129877385 (GRCh38)
- Gene constraint
- LOEUF 0.543 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 56.56 · 4 PDB
Similar variants
- NFRKB p.Arg792Gln Uncertain significance ★★ ⚠ same type
- NFRKB c.641-27A>C Uncertain significance ★ same type
- NFRKB p.Ala1057Thr Uncertain significance ★ ⚠ same type
- NFRKB p.Ala1118Val Uncertain significance ★ ⚠ same type
- NFRKB p.Ala1128Val Uncertain significance ★ ⚠ same type
- NFRKB p.Ala1148Pro Uncertain significance ★ ⚠ same type
- NFRKB p.Ala1159Ser Uncertain significance ★ ⚠ same type
- NFRKB p.Ala230Val 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/nfrkb-p-val504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown