ABL1 p.Ser1024=
c.3072C>T · rs34276964 · VCV736068
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.669%, afr)
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 -10 | GERP -3.8 |
| Overall | ||
| CADD | 0.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.669%
African / African-American · 502/75,072 alleles
Filtering AF
0.62%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.601%
Overall
0.0422%
681/1,613,650 alleles · rare
exomes 402/1,461,296 · genomes 279/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.669% | 150 |
| Ashkenazi Jewishnot grpmax-eligible | 0.263% | 380 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,084 |
| South Asian | 0.0274% | 3,643 |
| Admixed American | 0.025% | 4,002 |
| Middle Eastern | 0.0165% | 6,062 |
| European (non-Finnish) | 0.00254% | 39,335 |
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.Ser1024=
- Coding
- c.3072C>T
- MANE Select
- NM_005157
- dbSNP
- rs34276964
- Type
- single nucleotide variant
- Location
- chr9:130885362 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 85 PDB
- Residue 1024
- the 'f-actin-binding' region
Similar variants
- 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
- ABL1 p.Tyr226Cys 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/abl1-p-ser1024 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown