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MYCN
Final classification
VUS
MYCN c.1340T>C · p.Leu447Ser
MYCN

NM_005378.5:c.1340T>C (p.Leu447Ser) is a missense variant in MYCN, located within the C-terminal leucine zipper domain critical for protein dimerization and DNA binding. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.

Gene
MYCN
Transcript
NM_005378.5
HGVS · transcript:coding
NM_005378.5:c.1340T>C
Consequence
N/A
GRCh38
chr2:15946042 T>C
GRCh37
chr2:16086164 T>C
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: PM1 moderate, PM2 supporting; combination = 1 moderate + 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: PM1 moderate, PM2 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM1PM2 VUS
MYCN c.1340T>C

NM_005378.5:c.1340T>C (p.Leu447Ser) is a missense variant in MYCN, located within the C-terminal leucine zipper domain critical for protein dimerization and DNA binding. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.1 PM1 (moderate) is met: residue Leu447 lies within the MYCN leucine zipper domain, a well-established critical functional domain. The variant is absent from population databases, consistent with a lack of benign variation in this region.2 PM2 (supporting) is met: the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency <0.1%).3 PVS1 is not applicable: the variant is a missense substitution and does not qualify as a predicted null variant under PMC6185798.4 PP3 is not met: in silico predictors are conflicting (REVEL 0.767 damaging, BayesDel 0.164 neutral). BP4 is also not met for the same reason.5 BP1 is not met: missense variants in MYCN are a known disease mechanism for Feingold syndrome type 1 and megalencephaly-polydactyly syndrome. With one moderate criterion (PM1) and one supporting criterion (PM2), this combination does not reach the Likely Pathogenic threshold under generic ACMG/AMP 2015 combination rules (PMID:25741868). The variant is classified as a Variant of Uncertain Significance (VUS).6

PM1 + PM2 VUS
Gene diagram · NM_005378.5 · variants mapped to exon structure
MYCN NM_005378.5
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.767. BayesDel score = 0.163771.
      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. MYCN, a transcription factor, is altered by amplification and overexpression in a variety of cancer types including in neuroblastoma.
      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.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots