NM_004304.4:c.3373G>A

ALK · NP_004295.2:p.(Gly1125Ser) · NM_004304.4

GRCh37: chr2:29445460 C>T · GRCh38: chr2:29222594 C>T

Gene: ALK Transcript: NM_004304.4

Final call

VUS

PM2 supporting PP3 supporting

Variant details

Gene

ALK

Transcript

NM_004304.4

Protein

NP_004295.2:p.(Gly1125Ser)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_004304.4:c.3373G>A (p.Gly1125Ser) is a missense variant in exon 21 of ALK, residing within the tyrosine kinase domain P-loop (GAFGE motif). It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0, meeting PM2 at the supporting level.

In silico predictors support a deleterious effect: REVEL score 0.968 (strongly damaging) and BayesDel score 0.576 (damaging), meeting PP3 at the supporting level. SpliceAI predicts no splice impact (max delta 0.00).

No variant-specific functional data, de novo reports, segregation data, or case-control studies are available. The variant is absent from ClinVar, COSMIC, and cancerhotspots.org. OncoKB classifies it as 'Unknown Oncogenic Effect'.

With two supporting criteria (PM2_supporting + PP3_supporting) and no criteria met at moderate, strong, or benign levels, this variant is classified as a Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 generic classification rules (PMID:25741868).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_004304.4:c.3373G>A is a missense substitution (p.Gly1125Ser); it does not fall into the PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_variant_assessment pvs1_generic_framework
PS1	Not met	No alternate nucleotide change at c.3373 resulting in the same amino acid change has been identified as pathogenic in ClinVar or the literature.	clinvar
PS2	Not met	No de novo occurrence data are available for this variant; no family studies have been identified.
PS3	Not met	No variant-specific functional data have been identified. OncoKB classifies this variant as 'Unknown Oncogenic Effect' with no curated functional evidence. No experimental studies of NM_004304.4:c.3373G>A or a systematically characterized range encompassing Gly1125 were found in the literature.	oncokb
PS4	Not met	No case-control or cohort data demonstrating statistically significant enrichment of this variant in affected individuals versus controls are available.
PS5	Not met	No alternate missense change at codon 1125 has been reported as pathogenic in ClinVar or the literature. PM5 candidate review found no same-residue comparator variants.	pm5_candidates
PM1	Not met	Although Gly1125 resides within the ALK tyrosine kinase domain P-loop (GAFGE motif, aa 1125-1129), cancerhotspots.org does not identify this residue as a statistically significant hotspot, and no literature establishes that missense variants in the ALK kinase domain are a common mechanism of germline disease. Domain-level knowledge is insufficient for PM1 in the absence of enrichment-based or residue-specific evidence.
PM2	Met	NM_004304.4:c.3373G>A is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0, meeting the non-VCEP threshold for PM2 (allele frequency <0.1% or absent).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	No same-residue, same-reference-amino-acid comparator variants were identified in ClinVar; PM5 automatic candidate harvesting was unable to find eligible comparators.	pm5_candidates
PM6	Not met	No de novo occurrence data are available; no family studies or trio sequencing reports were identified.
PP1	Not met	No co-segregation data are available for this variant.
PP2	Not met	No missense constraint data (Z-score, missense depletion metrics) are available for ALK to assess whether the gene has a low rate of benign missense variation.
PP3	Met	In silico predictors support a deleterious effect: REVEL score 0.968 (above the 0.932 threshold commonly used for PP3) and BayesDel score 0.576 (above the 0.5 damaging threshold). SpliceAI predicts no splice impact (max delta 0.00).	revel bayesdel spliceai
PP4	Not met	No patient phenotype information is available to assess specificity for an ALK-related disorder.
PP5	Not met	No reputable source (ClinVar, diagnostic laboratory) has reported this variant as pathogenic.	clinvar
BA1	Not met	NM_004304.4:c.3373G>A is absent from all gnomAD datasets; allele frequency does not exceed the BA1 threshold of >1%.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	NM_004304.4:c.3373G>A is absent from all gnomAD datasets; allele frequency does not exceed the non-VCEP BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No data are available demonstrating this variant has been observed in a healthy adult individual for a fully penetrant disorder.
BS3	Not met	No well-established in vitro or in vivo functional studies demonstrate that this variant has no deleterious effect on protein function or splicing.
BS4	Not met	No family segregation data are available to demonstrate lack of co-segregation with disease.
BP1	Not met	ALK has well-established pathogenic missense variants (e.g., p.Arg1275Gln in neuroblastoma predisposition), so a missense variant does not qualify for BP1, which requires that primarily truncating variants cause disease.
BP2	Not met	No data are available to demonstrate this variant has been observed in trans with a known pathogenic variant in ALK.
BP4	Not met	In silico predictors do not support a benign effect; REVEL score of 0.968 is strongly damaging, and BayesDel score of 0.576 is above the damaging threshold.	revel bayesdel
BP5	Not met	No evidence that this variant was found in a case with an alternate molecular basis for disease.
BP6	Not met	No reputable source has classified this variant as benign; the variant is absent from ClinVar.	clinvar
BP7	N/A	NM_004304.4:c.3373G>A is a missense variant (p.Gly1125Ser), not synonymous or intronic; BP7 applies only to synonymous variants without predicted splice impact.
BP3	N/A	In-frame indel rule not applicable to a substitution variant.
PM3	N/A	No recessive inheritance data available; ALK germline disease is not known to follow a recessive pattern.
PM4	N/A	No protein-length change; this is a missense substitution.

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