ABL1 p.Ser749=
c.2247G>A · rs535696830 · VCV3021458
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, 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 -8.2 | GERP -3.8 |
| Overall | ||
| CADD | 1.294 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,882 alleles
Filtering AF
0.00883%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.00453%
73/1,613,196 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,610 |
| European (non-Finnish) | 0.00508% | 19,667 |
| Finnishnot grpmax-eligible | 0.00476% | 21,011 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,251 |
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
- ABL1
- Protein
- p.Ser749=
- Coding
- c.2247G>A
- MANE Select
- NM_005157
- dbSNP
- rs535696830
- Type
- single nucleotide variant
- Location
- chr9:130884537 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 85 PDB
- Residue 749
- the 'disordered' region
Similar variants
- ABL1 p.Ser749Leu Benign/Likely benign ★★ same residue
- ABL1 p.Ala337Thr Pathogenic ★★ ⚠ same type
- ABL1 p.Ala433Thr Likely pathogenic ★★ same type
- ABL1 p.Asp504Gly Likely pathogenic ★★ ⚠ same type
- ABL1 p.Glu509Lys Pathogenic/Likely pathogenic ★★ same type
- ABL1 p.Gly254Arg Pathogenic/Likely pathogenic ★★ same type
- ABL1 p.Pro230Leu Likely pathogenic ★★ same type
- ABL1 p.Trp99Arg 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/abl1-p-ser749 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown