Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.89%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6.7 | GERP 5.7, phastCons 1 |
| Overall | ||
| CADD | 8.858 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.89%
African / African-American · 2,168/75,036 alleles
Filtering AF
2.79%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.75%
Overall
0.353%
5,701/1,614,170 alleles · low-frequency
exomes 4,163/1,461,884 · genomes 1,538/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.89% | 35 |
| Ashkenazi Jewishnot grpmax-eligible | 2.63% | 38 |
| Middle Eastern | 1.22% | 82 |
| Remaining individualsnot grpmax-eligible | 0.693% | 144 |
| Admixed American | 0.686% | 146 |
| European (non-Finnish) | 0.153% | 654 |
| South Asian | 0.0285% | 3,503 |
| Finnishnot grpmax-eligible | 0.00781% | 12,809 |
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
- KEL
- Protein
- p.Arg516=
- Coding
- c.1546C>A
- MANE Select
- NM_000420
- dbSNP
- rs8176034
- Type
- single nucleotide variant
- Location
- chr7:142943829 (GRCh38)
- Gene constraint
- LOEUF 1.11 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.46
- Residue 516
- the peptidase m13 domain
Similar variants
- KEL p.Pro375Thr Uncertain significance ★★ ⚠ same type
- KEL p.Leu335= Likely benign ★★ same type
- KEL p.Leu597Pro Benign ★★ same type
- KEL p.Phe324= Benign ★★ same type
- KEL c.400+1G>A Pathogenic ★ same type
- KEL p.Ala148Gly Uncertain significance ★ ⚠ same type
- KEL p.Ala311Asp Uncertain significance ★ ⚠ same type
- KEL p.Ala311Val 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/kel-p-arg516 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown