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MYCN
Final classification
VUS
PM2PM4
MYCN
c.865_867del
p.Ser289del
This variant

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.

Transcript
NM_005378.6
HGVS · transcript:coding
NM_005378.6:c.865_867del
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 applied · 7 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is present at extremely low frequency in population databases. In gnomAD v2.1 the allele frequency is 0.00637% (2/31,376 alleles, 0 homozygotes) and in gnomAD v4.1 the allele frequency is 0.00043% (7/1,613,892 alleles, 0 homozygotes). Both are well below the 0.1% threshold, consistent with a rare variant absent from controls at appreciable frequency.
gnomAD v2.1: AF=6.37e-05 (0.00637%)2/31376 alleles
PM4 moderate Pathogenic
NM_005378.6:c.865_867del results in an in-frame deletion of a single amino acid (p.Ser289del) within MYCN exon 3. This changes the protein length in a non-repeat region of a gene where loss of function is an established disease mechanism for Feingold syndrome type 1.
In-frame single amino acid deletion (p.Ser289del) resulting in protein length changeNo evidence that position 289 lies within a repetitive regionMYCN LoF is an established mechanism for Feingold syndrome type 1 (autosomal dominant)
Assessed · not applied · 7 not met · 0 not assessed
Pathogenic
PVS1 NM_005378.6:c.865_867del is an in-frame deletion of a single amino acid (p.Ser289del) and does not fall into the default generic PVS1 null-variant categories of nonsense, frameshift, or canonical ±1,2 splice consensus variants.
PS4 No case-control or statistical evidence supports pathogenicity.
PM1 The variant does not lie within a statistically significant mutational hotspot or a well-established critical functional domain where all missense variation is known to be pathogenic.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
Benign
BA1 The allele frequency is far below the 1% threshold for BA1.
BS1 The allele frequency is below the 0.3% threshold.
BP4 Insufficient multiple lines of computational evidence support a benign effect.
N/A · 19 PS1 · PS2 · PS3 · PM3 · PM5 · PM6 · PP1 · PP2 · PP4 · PP5 · BS2 · BS3 · BS4 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
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