NM_004304.4:c.4033G>A

ALK · NP_004295.2:p.(Gly1345Arg) · NM_004304.4

GRCh37: chr2:29420448 C>T · GRCh38: chr2:29197582 C>T

Gene: ALK Transcript: NM_004304.4

Final call

VUS

PM2 supporting

Variant details

Gene

ALK

Transcript

NM_004304.4

Protein

NP_004295.2:p.(Gly1345Arg)

gnomAD AF

1.8589318577545341e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_004304.4:c.4033G>A (p.Gly1345Arg) is absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (AF 1.86 × 10⁻⁶, 3/1,613,830 alleles), meeting PM2 at supporting strength.

The variant is a missense substitution not located in a statistically significant mutational hotspot; PM1 is not met.

In silico predictions are conflicting: REVEL score 0.786 supports a deleterious effect, but BayesDel score 0.144 is in the benign range and SpliceAI max delta 0.20 is borderline. PP3 is not met, and BP4 is not met.

This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory, SCV002134937); no reputable source classifies it as pathogenic or benign. PP5 and BP6 are not met.

No variant-specific functional studies (PS3/BS3), segregation data (PP1/BS4), de novo observations (PS2/PM6), or case-control data (PS4) were identified. PVS1 is not applicable as this is a missense variant outside canonical null-variant categories.

With only PM2_Supporting met, the variant does not reach a Likely Pathogenic threshold (requiring at least 2 Supporting criteria or 1 Moderate + 1 Supporting under generic ACMG/AMP rules) nor a Likely Benign threshold. The variant remains a Variant of Uncertain Significance.

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.4033G>A is a missense variant (p.Gly1345Arg); it does not fall into the null-variant categories of nonsense, frameshift, or canonical ±1,2 splice consensus variants required for PVS1 under the ClinGen SVI PVS1 decision framework (PMC6185798).	pvs1_generic_framework
PS1	Not assessed	No evidence was identified for an established pathogenic variant with the same amino acid change (p.Gly1345Arg) resulting from a different nucleotide substitution. No literature or database reports a pathogenic G1345 variant at a different nucleotide position.
PS2	Not assessed	No de novo observation with confirmed maternity and paternity was identified for this variant in any source.
PS3	Not met	No variant-specific well-established in vitro or in vivo functional studies were identified. OncoKB reports Unknown Oncogenic Effect with no variant-specific reviewed functional evidence. SpliceAI delta score of 0.20 does not independently constitute functional evidence.	oncokb spliceai
PS4	Not assessed	No case-control studies or cohort data comparing variant prevalence in affected versus unaffected individuals were identified. ClinVar contains a single clinical laboratory submission (Labcorp/Invitae) classifying the variant as Uncertain significance, but this does not provide case counts for PS4.	clinvar
PS5	N/A	PS5 is not a criterion defined in the generic ACMG/AMP 2015 framework (Richards et al., PMID:25741868). No VCEP/CSPEC framework with PS5 is available for ALK.	generic_acmg_combination_rules
PM1	Not met	The variant is not located in a statistically significant mutational hotspot. Although p.Gly1345 resides in the C-terminal region of the ALK tyrosine kinase domain, no functional domain-level PM1 assignment has been established by a CSPEC/VCEP, and hotspots analysis did not identify this residue as significant.
PM2	Met	NM_004304.4:c.4033G>A is absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (overall AF = 1.86 × 10⁻⁶, 3/1,613,830 alleles; highest subpopulation frequency = 2.54 × 10⁻⁶ in European non-Finnish; grpmax FAF = 6.8 × 10⁻⁷). This frequency is well below the non-VCEP PM2 supporting threshold of <0.1%.	gnomad_v2 gnomad_v4
PM5	N/A	No same-residue comparator missense variants with prior pathogenic classification were identified. PM5 candidate search returned no eligible comparators; automatic candidate harvesting was skipped due to inability to confirm classic same-residue PM5 semantics.	pm5_candidates
PM6	Not assessed	No assumed de novo observations (without confirmed maternity/paternity) were identified for this variant in any source.
PP1	Not assessed	No cosegregation data in multiple affected family members were identified for this variant.
PP2	Not assessed	HCI prior probability is not available for ALK (gene not supported). No CSPEC/VCEP PP2 rule is available. Without gene-level missense constraint metrics (e.g., Z-score, oe ratio), PP2 cannot be reliably assessed.
PP3	Not met	In silico predictions are conflicting and do not provide multiple concordant lines of computational evidence for a deleterious effect. REVEL score 0.786 supports pathogenicity, but BayesDel score 0.144 falls in the benign range, and SpliceAI max delta 0.20 is at the threshold of significance (DL 0.20, AL 0.15).	revel bayesdel spliceai
PP4	Not assessed	No patient phenotype or family history data are available to assess whether the phenotype is highly specific for a disease with a single genetic etiology.
PP5	Not met	No reputable source classifies this variant as pathogenic. ClinVar reports a single submission from Labcorp Genetics (formerly Invitae) classifying it as Uncertain significance (SCV002134937). PMID:28492532 is the Sherloc methodology paper and does not report this specific variant. PMID:20301782 is a GeneReviews chapter on ALK-related neuroblastic tumor susceptibility; its abstract does not mention this variant, and no full text is available to confirm variant-specific reporting.	clinvar
BA1	Not met	The variant is absent from gnomAD v2.1 and present at AF = 1.86 × 10⁻⁶ in gnomAD v4.1, far below the BA1 threshold of >1% (and the more conservative >5%).	gnomad_v2 gnomad_v4
BS1	Not met	The variant frequency in gnomAD v4.1 (AF = 1.86 × 10⁻⁶, 0.00019%) is far below the non-VCEP BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4
BS2	Not met	Observation of the variant at very low frequency in population databases (3 heterozygous alleles in gnomAD v4.1) does not meet BS2, which requires confirmed observation in a healthy adult individual for a disorder expected to be fully penetrant at an early age. The gnomAD population data lack phenotype confirmation and no homozygous observations were recorded.	gnomad_v4
BS3	Not assessed	No well-established in vitro or in vivo functional studies demonstrating no damaging effect on protein function or splicing were identified for this variant.
BS4	Not assessed	No segregation data in affected family members are available to assess lack of cosegregation with disease.
BP1	Not met	ALK-related neuroblastic tumor susceptibility is not a disorder where only truncating variants cause disease. Germline ALK pathogenic variants include both activating missense mutations in the tyrosine kinase domain and potential loss-of-function variants. Therefore, a missense variant does not meet BP1.	pvs1_gene_context
BP2	Not assessed	No data are available regarding observation of this variant in trans with a pathogenic variant for a fully penetrant dominant disorder.
BP3	N/A	In-frame deletions/insertions in a repetitive region without a known function — not applicable to this substitution variant.
BP4	Not met	Multiple lines of computational evidence do not concordantly suggest no impact on the gene product. REVEL score 0.786 supports a deleterious effect, contradicting BP4. BayesDel 0.144 is in the benign range, and SpliceAI delta 0.20 is borderline. The computational evidence is conflicting rather than consistently benign.	revel bayesdel spliceai
BP5	Not assessed	No data are available regarding observation of this variant in a case with an alternate molecular basis for disease.
BP6	Not met	No reputable source classifies this variant as benign. ClinVar reports Uncertain significance from a single clinical laboratory (Labcorp/Invitae, SCV002134937).	clinvar
BP7	N/A	This is a missense variant (c.4033G>A, p.Gly1345Arg), not a synonymous variant. BP7 applies only to synonymous variants without predicted splice impact.

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