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MYCN
Final classification
VUS
MYCN c.865_867del · p.Ser289del
MYCN

NM_005378.6:c.865_867del (p.Ser289del) is an in-frame deletion of a single amino acid in exon 3 of MYCN, a gene in which loss-of-function variants cause autosomal dominant Feingold syndrome type 1.

Gene
MYCN
Transcript
NM_005378.6
HGVS · transcript:coding
NM_005378.6:c.865_867del
Consequence
N/A
GRCh38
chr2:15945560 TTCC>T
GRCh37
chr2:16085682 TTCC>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, PM4 moderate; 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: PM2 supporting, PM4 moderate; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM2PM4 VUS
MYCN c.865_867del

NM_005378.6:c.865_867del (p.Ser289del) is an in-frame deletion of a single amino acid in exon 3 of MYCN, a gene in which loss-of-function variants cause autosomal dominant Feingold syndrome type 1.1 This variant does not meet PVS1 criteria as it is not a null variant (nonsense, frameshift, or canonical splice site).2 The variant is present at extremely low frequency in population databases: gnomAD v2.1 AF = 0.00637% (2/31,376 alleles) and gnomAD v4.1 AF = 0.00043% (7/1,613,892 alleles), with no homozygotes observed, meeting PM2 at supporting strength.3 The in-frame deletion changes protein length (p.Ser289del) in a non-repeat region of MYCN, meeting PM4 at moderate strength.4 No variant-specific functional studies, segregation data, de novo observations, or case-control evidence are available. ClinVar reports a single classification of uncertain significance.5 Computational evidence is limited: SpliceAI predicts no splicing impact (max delta = 0.04), and REVEL/BayesDel are not applicable to deletions. PP3 and BP4 are not met.6 Overall classification: Uncertain Significance. One moderate criterion (PM4) and one supporting criterion (PM2) are met, which is insufficient to reach likely pathogenic or likely benign under the ACMG/AMP 2015 framework.7

PM2 + PM4 VUS
1 pvs1_gene_context
2 pvs1_variant_assessment
4 pvs1_gene_context
7 generic_acmg_combination_rules
Gene diagram · NM_005378.6 · variants mapped to exon structure
MYCN NM_005378.6
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
      This variant is present in gnomAD v4.1 (AF= 4.33734e-06; MAF= 0.00043%, 7/1613892 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 6.40123e-05; MAF= 0.00640%, 4/62488 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 6.3743e-05; MAF= 0.00637%, 2/31376 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000129685; MAF= 0.01297%, 2/15422 alleles, homozygotes = 0); grpmax FAF= 2.241e-05.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00043% · 7 / 1,613,892
      0 hom · FAF 6.8e-05%
      Remaining individuals
      4 / 62,488
      0.0064%
      European (non-Finnish)
      3 / 1,179,982
      0.00025%
      + 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0064% · 2 / 31,376
      0 hom · FAF 0.0022%
      European (non-Finnish)
      2 / 15,422
      0.013%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      Error retrieving ClinVar entry.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04).
      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
      Triaged references · 1 PMID not cited in assessment
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR