Starting
Initialising…
0%
ALK
Final classification
VUS
ALK c.4033G>A · p.Gly1345Arg
ALK

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.

Gene
ALK
Transcript
NM_004304.4
HGVS · transcript:coding
NM_004304.4:c.4033G>A
Consequence
N/A
GRCh38
chr2:29197582 C>T
GRCh37
chr2:29420448 C>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
ALK c.4033G>A

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.1 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.2 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.3 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.4 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.5

PM2 VUS
2 revelbayesdelspliceai ↗
4 pvs1_generic_framework ↗oncokb ↗pvs1_variant_assessment
5 generic_acmg_combination_rules
Gene diagram · NM_004304.4 · variants mapped to exon structure
ALK NM_004304.4
Fetching transcript structure from UCSC…
Applied criteria · 1 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Overall AF
      3 / 1,613,830
      0.00019%
      Highest · European (non-Finnish)
      0.00025%
      Homozygotes
      0
      grpmax FAF
      6.8e-05%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 1 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 3 / 1,180,024 0.00025% 0
      Admixed American 0 / 60,030
      European (Finnish) 0 / 64,038
      Amish 0 / 912
      East Asian 0 / 44,884
      Middle Eastern 0 / 5,784
      South Asian 0 / 91,056
      Ashkenazi Jewish 0 / 29,604
      African/African American 0 / 75,022
      This variant is present in gnomAD v4.1 (AF= 1.85893e-06; MAF= 0.00019%, 3/1613830 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.54232e-06; MAF= 0.00025%, 3/1180024 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 1363092)
      SpliceAI screenshot
      In silico
      SpliceAI predicts possible splice impact for this variant (max delta score = 0.20). REVEL score = 0.786. BayesDel score = 0.144187.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. ALK, a receptor tyrosine kinase, is recurrently altered by chromosomal rearrangements in various cancer types including anaplastic large cell lymphoma
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · 2 PMIDs triaged · 1 high-priority
      2papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      20301782 ↗ case observation
      Untitled reference
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots