ASXL2 p.Leu1237=
c.3709T>C · rs368648407 · VCV1542974
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
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 0.62 | GERP -0.077, phastCons 0.009 |
| Overall | ||
| CADD | 1.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,890 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.00124%
20/1,613,846 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,963 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,466 |
| African / African-American | 0.00134% | 74,902 |
| European (non-Finnish) | 0.00127% | 78,660 |
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
- ASXL2
- Protein
- p.Leu1237=
- Coding
- c.3709T>C
- MANE Select
- NM_018263
- dbSNP
- rs368648407
- Type
- single nucleotide variant
- Location
- chr2:25742628 (GRCh38)
- Gene constraint
- LOEUF 0.239 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 47.17 · 1 PDB
Similar variants
- ASXL2 p.Ala1372Gly Uncertain significance ★★ ⚠ same type
- ASXL2 p.Ala336Ser Uncertain significance ★★ ⚠ same type
- ASXL2 p.Ala682Thr Uncertain significance ★★ ⚠ same type
- ASXL2 p.Ala844Pro Uncertain significance ★★ ⚠ same type
- ASXL2 p.Arg252Lys Uncertain significance ★★ ⚠ same type
- ASXL2 p.Asn803Lys Uncertain significance ★★ ⚠ same type
- ASXL2 p.Asp1165Glu Uncertain significance ★★ ⚠ same type
- ASXL2 p.Asp1420Gly 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/asxl2-p-leu1237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown