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ERBB2
Final classification
VUS
ERBB2 c.3582del · p.Glu1195SerfsTer3
ERBB2

NM_004448.3:c.3582del (p.Glu1195SerfsTer3) is a frameshift deletion in exon 27 of ERBB2, the last exon, predicted to truncate 58 C-terminal residues without triggering nonsense-mediated decay.

Gene
ERBB2
Transcript
NM_004448.3
HGVS · transcript:coding
NM_004448.3:c.3582del
Consequence
N/A
GRCh38
chr17:39727854 AC>A
GRCh37
chr17:37884107 AC>A
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: PVS1 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: PVS1 moderate, PM2 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
ERBB2 c.3582del

NM_004448.3:c.3582del (p.Glu1195SerfsTer3) is a frameshift deletion in exon 27 of ERBB2, the last exon, predicted to truncate 58 C-terminal residues without triggering nonsense-mediated decay.1 Under the ClinGen SVI PVS1 framework (PMC6185798), the variant qualifies for PVS1 at moderate strength: a frameshift in the last exon where NMD is not predicted and the truncated region (<10% of the protein) does not contain a critical functional domain — the kinase domain remains intact.2 The variant is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada), supporting PM2 at supporting strength.3 No functional studies, case-control data, de novo observations, cosegregation data, or ClinVar classifications are available for this variant. Computational splicing prediction (SpliceAI max delta = 0.00) is neutral.4 The combined evidence (PVS1_Moderate + PM2_Supporting) yields 1 moderate and 1 supporting criterion. Under generic ACMG/AMP 2015 combination rules, this does not meet the threshold for Likely Pathogenic (requires ≥1 moderate + ≥4 supporting, or ≥2 moderate + ≥2 supporting, among other combinations). The variant is classified as a Variant of Uncertain Significance (VUS).5 Human review is recommended: ERBB2 is a proto-oncogene where C-terminal truncations have been associated with gain-of-function in somatic contexts, and the evidence for germline ERBB2 loss-of-function as a disease mechanism is limited.6

PVS1 + PM2 VUS
1 pvs1_variant_assessment
5 generic_acmg_combination_rules
6 pvs1_gene_context
Gene diagram · NM_004448.3 · variants mapped to exon structure
ERBB2 NM_004448.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 18 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 moderate review Pathogenic
NM_004448.3:c.3582del is a frameshift deletion in exon 27/27 (the last exon) of ERBB2, predicted to result in p.(Glu1195SerfsTer3) with loss of 58 C-terminal residues (1195-1255). The variant is located in the last exon and is not predicted to undergo nonsense-mediated decay. Under PMC6185798, for frameshift variants where NMD is not expected and the truncated region (<10% of the protein) does not remove a critical functional domain (the kinase domain, aa 720-987, remains intact), PVS1 is applied at moderate strength. Germline ERBB2 loss-of-function is supported as a disease mechanism by targeted literature review, though the supporting evidence is predominantly derived from related ERBB-family genes and somatic cancer contexts.
Frameshift variant in last exon (27/27)NMD not predictedTruncation removes 58 C-terminal residues (~4.6% of protein)
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, consistent with a rare pathogenic variant. Under generic ACMG/AMP, absence from population databases (allele frequency <0.1%) supports PM2 at supporting strength.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes)Absent from gnomAD-Canada v1.0
Assessed · not applied
Pathogenic
PS2 No de novo occurrence data is available for this variant.
PS3 No functional studies testing NM_004448.3:c.3582del or a systematically characterized range that includes this position were identified in the literature.
PS4 No case-control data or statistical evidence of enrichment in affected individuals is available for this variant.
PM1 The variant does not lie within a statistically significant mutational hotspot as determined by cancerhotspots.org.
PM6 No de novo occurrence data is available for this variant.
PP1 No cosegregation data with disease is available for this variant.
PP3 SpliceAI predicts no splicing impact (max delta score = 0.00).
PP4 No patient-specific phenotype or family history data is available for assessment.
PP5 This variant is absent from ClinVar; no reputable source has reported it as pathogenic.
Benign
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 The variant is absent from gnomAD.
BS2 Not observed in a healthy adult homozygous or hemizygous state.
BS3 No well-established functional studies demonstrating a benign effect for this variant are available.
BS4 No cosegregation data demonstrating absence of segregation with disease is available.
BP2 No evidence of this variant occurring in trans with a known pathogenic variant in a recessive disorder.
BP4 SpliceAI predicts no splicing impact (max delta = 0.00), but NM_004448.3:c.3582del is a frameshift variant with a clear predicted protein-truncating effect (p.Glu1195SerfsTer3).
BP5 No alternative molecular cause has been identified in a case harboring this variant.
BP6 This variant is absent from ClinVar; no reputable source has reported it as benign.
N/A · 7 PS1 · PM4 · PM5 · PP2 · BP1 · BP3 · BP7
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 = 0.00).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
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