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ERBB3
Final classification
VUS
ERBB3 c.244G>A · p.Glu82Lys
ERBB3

NM_001982.3:c.244G>A (p.Glu82Lys) is a missense variant in ERBB3 exon 3.

Gene
ERBB3
Transcript
NM_001982.3
HGVS · transcript:coding
NM_001982.3:c.244G>A
Consequence
N/A
GRCh38
chr12:56085004 G>A
GRCh37
chr12:56478788 G>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: PM2 moderate, PP3 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: PM2 moderate, PP3 supporting; combination = 1 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
ERBB3 c.244G>A

NM_001982.3:c.244G>A (p.Glu82Lys) is a missense variant in ERBB3 exon 3. This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (0 alleles across all populations), meeting PM2 at moderate strength.1 Multiple in silico predictors support a deleterious effect: REVEL score 0.948 (strongly pathogenic) and BayesDel score 0.443 (intermediate, leaning deleterious), meeting PP3 at supporting strength.2 PVS1 is not applicable as c.244G>A is a missense variant, not a null variant (nonsense, frameshift, or canonical ±1,2 splice). Per ClinGen SVI PVS1 recommendations (PMC6185798), the generic PVS1 framework applies only to predicted null variants.3 The variant is absent from ClinVar, absent from COSMIC, and not located in a statistically significant mutational hotspot (CancerHotspots). No literature PMIDs were identified for this variant. OncoKB classifies it as 'Unknown Oncogenic Effect' without variant-specific functional evidence.4 No de novo, segregation, case-control, functional, or phenotype-specific data are available for this variant; PS2, PS3, PS4, PP1, PP4, PM6, and benign criteria BS2-BS4, BP5-BP6 remain not assessed. PM5 is not applicable as no pathogenic missense comparator at ERBB3 residue E82 was identified. BP7 is not applicable to missense variants.5 Overall classification: 1 moderate pathogenic criterion (PM2) and 1 supporting pathogenic criterion (PP3) are met. Under the generic ACMG/AMP 2015 combination rules (PMID:25741868), this does not reach the Likely Pathogenic threshold (minimum: 3 moderate, or 2 moderate + 2 supporting, or 1 moderate + 4 supporting). The variant is classified as a Variant of Uncertain Significance (VUS).6

PM2 + PP3 VUS
2 revelbayesdel
3 pvs1_generic_framework ↗pvs1_variant_assessment
5 pm5_candidates
6 generic_acmg_combination_rules
Gene diagram · NM_001982.3 · variants mapped to exon structure
ERBB3 NM_001982.3
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 = 0.00). REVEL score = 0.948. BayesDel score = 0.443228.
      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. ERBB3, a receptor tyrosine kinase, is altered by mutation or amplification in various cancer types.
      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