Is ALK p.Asp70Asn (c.208G>A) pathogenic?

ALK p.Asp70Asn (c.208G>A) is classified Conflicting classifications of pathogenicity in ALK (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-07-23). AlphaMissense: likely benign (0.148); Very rare (popmax 0.00223%, eas); Associated with neuroblastoma, susceptibility to, 3.

What condition is associated with ALK p.Asp70Asn (c.208G>A)?

ALK p.Asp70Asn (c.208G>A) is associated with neuroblastoma, susceptibility to, 3, hereditary neoplastic syndrome (ClinVar).

How common is ALK p.Asp70Asn (c.208G>A) in the general population?

ALK p.Asp70Asn (c.208G>A) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about ALK p.Asp70Asn (c.208G>A)?

AlphaMissense predicts likely benign (score 0.148) — an in-silico prediction, not a clinical call.

ALK p.Asp70Asn

c.208G>A · rs1365620880 · VCV1043891

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.148 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

neuroblastoma, susceptibility to, 3

Computational evidence

Protein change
AlphaMissense	0.148	likely benign
REVEL	0.065	moderately benign-leaning
SaProt	LLR -6.75	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 7.5	GERP 1.9, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 670 kb · p 0.12 · regional, not allelic
Overall
CADD	25.1	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 0.00223% East Asian · 1/44,760 alleles

Overall 0.000124% 2/1,611,170 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,760
Admixed American	0.00167%	59,818

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: ALK
Protein: p.Asp70Asn
Coding: c.208G>A
MANE Select: NM_004304
dbSNP: rs1365620880
Type: single nucleotide variant
Location: chr2:29920452 (GRCh38)
Gene constraint: LOEUF 0.562 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 68.26 · 79 PDB
Residue 70: the 'heparin-binding region' region

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

Disease context

neuroblastoma, susceptibility to, 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

Similar variants

ALK p.Asp70= Likely benign ★★ same residue
ALK p.Asp70Ala Uncertain significance ★ ⚠ same residue
ALK p.Asp70Glu Uncertain significance ★ ⚠ same residue
ALK p.Asp70Gly Uncertain significance ★ ⚠ same residue
ALK p.Arg1275Gln Pathogenic ★★ same condition
ALK c.1154+5G>A Uncertain significance ★★ same condition
ALK c.1155-3C>T Uncertain significance ★★ same condition
ALK c.1282+3A>G 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/alk-p-asp70asn (accessed [today's date]).

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