ABL1 p.Ser972=
c.2916G>A · rs143132804 · VCV781935
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.11%, 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 -4.9 | GERP -3.2 |
| Overall | ||
| CADD | 0.164 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.11%
African / African-American · 833/75,040 alleles
Filtering AF
1.05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.02%
Overall
0.361%
5,832/1,613,554 alleles · low-frequency
exomes 5,104/1,461,242 · genomes 728/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.11% | 90 |
| European (non-Finnish) | 0.373% | 268 |
| Ashkenazi Jewishnot grpmax-eligible | 0.365% | 274 |
| Finnishnot grpmax-eligible | 0.339% | 295 |
| Remaining individualsnot grpmax-eligible | 0.274% | 366 |
| Admixed American | 0.148% | 674 |
| South Asian | 0.011% | 9,108 |
| East Asian | 0.00223% | 44,874 |
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.Ser972=
- Coding
- c.2916G>A
- MANE Select
- NM_005157
- dbSNP
- rs143132804
- Type
- single nucleotide variant
- Location
- chr9:130885206 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 85 PDB
- Residue 972
- the 'disordered' region; the 'f-actin-binding' region; a UniProt-annotated variant site (in)
Similar variants
- ABL1 p.Ser972Leu Benign ★★ same residue
- ABL1 p.Ser972Pro Uncertain significance ★ ⚠ 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
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-ser972 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown