ABL1 p.Thr700=
c.2100C>T · rs374980809 · VCV2070112
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.111%, sas)
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 -3 | GERP -3.5 |
| Overall | ||
| CADD | 3.026 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.111%
South Asian · 101/91,052 alleles
Filtering AF
0.0933%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0869%
Overall
0.0131%
211/1,611,924 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.111% | 902 |
| Middle Eastern | 0.0992% | 1,008 |
| African / African-American | 0.0893% | 1,120 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,805 |
| East Asian | 0.00669% | 14,949 |
| Admixed American | 0.00667% | 14,989 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,578 |
| European (non-Finnish) | 0.00136% | 73,740 |
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.Thr700=
- Coding
- c.2100C>T
- MANE Select
- NM_005157
- dbSNP
- rs374980809
- Type
- single nucleotide variant
- Location
- chr9:130884390 (GRCh38)
- Gene constraint
- LOEUF 0.19 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.68 · 85 PDB
- Residue 700
- the 'disordered' region
Similar variants
- ABL1 p.Thr700Ala 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-thr700 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown