Is ABL1 p.Asn670Ser (c.2009A>G) pathogenic?

ABL1 p.Asn670Ser (c.2009A>G) is classified Likely benign in ABL1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-21). AlphaMissense: likely benign (0.0755); Ultra-rare (popmax 0.0716%, sas); Associated with Inborn genetic diseases.

What condition is associated with ABL1 p.Asn670Ser (c.2009A>G)?

ABL1 p.Asn670Ser (c.2009A>G) is associated with Inborn genetic diseases (ClinVar).

How common is ABL1 p.Asn670Ser (c.2009A>G) in the general population?

ABL1 p.Asn670Ser (c.2009A>G) is ultra-rare (popmax 0.0716%, sas) (gnomAD).

What do computational predictors say about ABL1 p.Asn670Ser (c.2009A>G)?

AlphaMissense predicts likely benign (score 0.0755) — an in-silico prediction, not a clinical call.

ABL1 p.Asn670Ser

c.2009A>G · rs61746126 · VCV133434

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0755 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0716%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0755	likely benign
REVEL	0.113	moderately benign-leaning
SaProt	LLR -6.20	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 5,156 bp · p 0.054 · regional, not allelic
Overall
CADD	20.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0716% South Asian · 65/90,736 alleles

Filtering AF 0.0576% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0526%

Overall 0.0419% 674/1,609,178 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0716%	1,396
Remaining individualsnot grpmax-eligible	0.053%	1,886
European (non-Finnish)	0.0438%	2,283
Admixed American	0.0353%	2,834
East Asian	0.0312%	3,200
African / African-American	0.0281%	3,563
Middle Eastern	0.0166%	6,024
Ashkenazi Jewishnot grpmax-eligible	0.0068%	14,700
Finnishnot grpmax-eligible	0.00159%	62,856

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.Asn670Ser
Coding: c.2009A>G
MANE Select: NM_005157
dbSNP: rs61746126
Type: single nucleotide variant
Location: chr9:130884299 (GRCh38)
Gene constraint: LOEUF 0.19 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 64.68 · 85 PDB
Residue 670: the 'disordered' region

Full ABL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABL1 p.Ala767Val Uncertain significance ★★ ⚠ same condition
ABL1 p.Arg1016His Uncertain significance ★★ ⚠ same condition
ABL1 p.Arg771Gly Uncertain significance ★★ ⚠ same condition
ABL1 p.Asn1088His Uncertain significance ★★ ⚠ same condition
ABL1 p.Asn120Thr Uncertain significance ★★ ⚠ same condition
ABL1 p.Asn414Lys Uncertain significance ★★ ⚠ same condition
ABL1 p.Glu123Gln Uncertain significance ★★ ⚠ same condition
ABL1 p.Gly677Arg Uncertain significance ★★ ⚠ same condition

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-asn670ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown