Is ABL2 p.Lys930Arg (c.2789A>G) pathogenic?

ABL2 p.Lys930Arg (c.2789A>G) is classified Benign in ABL2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2023-07-01). AlphaMissense: likely benign (0.1402); Low-frequency (popmax 2.64%, mid).

How common is ABL2 p.Lys930Arg (c.2789A>G) in the general population?

ABL2 p.Lys930Arg (c.2789A>G) is low-frequency (popmax 2.64%, mid) (gnomAD).

What do computational predictors say about ABL2 p.Lys930Arg (c.2789A>G)?

AlphaMissense predicts likely benign (score 0.1402) — an in-silico prediction, not a clinical call.

ABL2 p.Lys930Arg

c.2789A>G · rs17277288 · VCV770497

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.1402 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.64%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1402	likely benign
REVEL	0.07	moderately benign-leaning
SaProt	LLR -6.34	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 4.1	GERP 1.1, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 2,725 bp · p 0.85 · regional, not allelic
Overall
CADD	23.7	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 2.64% Middle Eastern · 160/6,062 alleles

Filtering AF 2.31% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.18%

Overall 1.22% 19,751/1,614,164 alleles · low-frequency exomes 18,416/1,461,888 · genomes 1,335/152,276 · joint denominator

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	2.96%	34
Middle Easterngrpmax	2.64%	38
European (non-Finnish)	1.45%	69
Remaining individualsnot grpmax-eligible	1.22%	82
Admixed American	0.973%	103
Ashkenazi Jewishnot grpmax-eligible	0.773%	129
South Asian	0.65%	154
African / African-American	0.253%	395
Finnishnot grpmax-eligible	0.219%	457
East Asian	0.00223%	44,884

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ABL2
Protein: p.Lys930Arg
Coding: c.2789A>G
MANE Select: NM_007314
dbSNP: rs17277288
Type: single nucleotide variant
Location: chr1:179108478 (GRCh38)
Gene constraint: LOEUF 0.578 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 60.19 · 9 PDB
Residue 930: the 'f-actin-binding' region; a UniProt-annotated variant site (in)

Full ABL2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABL2 c.*4125A>G Benign ★★ same type
ABL2 p.Thr784Ser Likely benign ★★ same type
ABL2 p.Ala1029Thr Uncertain significance ★ ⚠ same type
ABL2 p.Ala1076Thr Uncertain significance ★ ⚠ same type
ABL2 p.Ala1156Val Uncertain significance ★ ⚠ same type
ABL2 p.Ala38Ser Uncertain significance ★ ⚠ same type
ABL2 p.Ala445Thr Uncertain significance ★ ⚠ same type
ABL2 p.Ala622Thr Uncertain significance ★ ⚠ 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/abl2-p-lys930arg (accessed [today's date]).

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