SETD5 p.Arg283=
c.849G>A · rs17050347 · VCV1168744
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.03%, sas)
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 0.93 | GERP -3.5, phastCons 1 |
| Overall | ||
| CADD | 7.063 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.03%
South Asian · 3,672/91,082 alleles
Filtering AF
3.92%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.88%
Overall
1.48%
23,954/1,613,934 alleles · low-frequency
exomes 22,320/1,461,632 · genomes 1,634/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 4.03% | 25 |
| Amishnot grpmax-eligible | 3.4% | 29 |
| Middle Eastern | 3% | 33 |
| Remaining individualsnot grpmax-eligible | 1.55% | 65 |
| European (non-Finnish) | 1.5% | 67 |
| Ashkenazi Jewishnot grpmax-eligible | 1.22% | 82 |
| Finnishnot grpmax-eligible | 0.862% | 116 |
| Admixed American | 0.63% | 159 |
| African / African-American | 0.225% | 444 |
| East Asian | 0.00891% | 11,220 |
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
- SETD5
- Protein
- p.Arg283=
- Coding
- c.849G>A
- MANE Select
- NM_001080517
- dbSNP
- rs17050347
- Type
- single nucleotide variant
- Location
- chr3:9441631 (GRCh38)
- Gene constraint
- LOEUF 0.376 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 47.10
- Residue 283
- the set domain
Similar variants
- SETD5 p.Arg283Trp Uncertain significance ★★ ⚠ same residue
- SETD5 p.Arg283Gln Likely benign ★ ⚠ same residue
- SETD5 c.1441-1G>A Pathogenic ★★ same type
- SETD5 c.1525-1G>C Pathogenic/Likely pathogenic ★★ same type
- SETD5 c.2347-1G>A Pathogenic ★★ same type
- SETD5 c.2347-7A>G Pathogenic ★★ same type
- SETD5 c.3631+1G>A Pathogenic ★★ same type
- SETD5 c.960-5C>G Pathogenic/Likely pathogenic ★★ 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/setd5-p-arg283 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown