Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Common
common (popmax 75.8%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
Luscan-Lumish syndrome
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 0.35 | GERP -4.5, phastCons 0.79 |
| Overall | ||
| CADD | 3.297 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
75.8%
African / African-American · 56,799/74,912 alleles
Filtering AF
75.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 75.1%
Overall
61.3%
988,241/1,613,356 alleles · common
exomes 888,970/1,461,350 · genomes 99,271/152,006 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 75.8% | 1 |
| Admixed American | 72.2% | 1 |
| East Asian | 70.4% | 1 |
| Finnishnot grpmax-eligible | 62.6% | 2 |
| Remaining individualsnot grpmax-eligible | 61.1% | 2 |
| European (non-Finnish) | 59.6% | 2 |
| South Asian | 59.6% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 59% | 2 |
| Middle Eastern | 53.1% | 2 |
| Amishnot grpmax-eligible | 42.1% | 2 |
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
- SETD2
- Protein
- p.Asn1155=
- Coding
- c.3465T>C
- MANE Select
- NM_014159
- dbSNP
- rs6767907
- Type
- single nucleotide variant
- Location
- chr3:47121171 (GRCh38)
- Gene constraint
- LOEUF 0.176 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.81 · 43 PDB
- Residue 1155
- a UniProt-annotated variant site (in aml; uncertain significance; somatic mutation); the 'disordered' region; a UniProt-annotated variant site (in all; uncertain significance; somatic mutation)
Similar variants
- SETD2 p.Arg1598Ter Pathogenic/Likely pathogenic ★★ same condition
- SETD2 p.Arg1740Gln Pathogenic ★★ ⚠ same condition
- SETD2 p.Arg1740Trp Pathogenic/Likely pathogenic ★★ same condition
- SETD2 p.Ala1121Thr Uncertain significance ★★ ⚠ same condition
- SETD2 p.Ala679Val Uncertain significance ★★ ⚠ same condition
- SETD2 p.Arg1065Cys Uncertain significance ★★ same condition
- SETD2 p.Arg329Gln Uncertain significance ★★ ⚠ same condition
- SETD2 p.Arg368Gln Uncertain significance ★★ ⚠ same condition
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/setd2-p-asn1155 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown