Starting
Initialising…
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PTEN
Final classification
VUS
PTEN c.348del · p.Asp116GlufsTer18
PTEN

NM_000314.8:c.348del predicts PTEN p.(Asp116GlufsTer18), a frameshift expected to truncate the protein early in exon 5.

Gene
PTEN
Transcript
NM_000314.8
HGVS · transcript:coding
NM_000314.8:c.348del
Consequence
N/A
GRCh38
chr10:87933106 AC>A
GRCh37
chr10:89692863 AC>A
Basis Generic ACMG/AMP 2015 combination rules fallback was used because no explicit PTEN VCEP-specific final classification framework was retrieved in the workspace. Under the retrieved generic_acmg_combination_rules, the applied evidence set is PVS1 plus PM2_Supporting, which does not meet a defined Pathogenic or Likely Pathogenic combination.
Generic ACMG/AMP 2015 combination rules fallback was used because no explicit PTEN VCEP-specific final classification framework was retrieved in the workspace. Under the retrieved generic_acmg_combination_rules, the applied evidence set is PVS1 plus PM2_Supporting, which does not meet a defined Pathogenic or Likely Pathogenic combination.
Classification rationale
PVS1PM2 VUS
PTEN c.348del

NM_000314.8:c.348del predicts PTEN p.(Asp116GlufsTer18), a frameshift expected to truncate the protein early in exon 5. The PTEN PVS1 decision tree assigns PVS1 to frameshift variants in NM_000314.8 when the stop/disruption occurs at or 5' to p.D375 (c.1121); this variant truncates at p.Asp116fs, which is well upstream of that threshold and is consistent with loss of function.1 The variant is absent from gnomAD v2.1 and gnomAD v4.1, and the PTEN specification applies PM2 at Supporting strength for variants with allele frequency below 0.00001, with a subpopulation threshold below 0.00002 when multiple alleles are present.2 No PTEN-specific final classification framework was retrieved, so the generic ACMG/AMP combination rules were used as fallback; with PVS1 and PM2_Supporting alone, this evidence set does not reach a defined pathogenic or likely pathogenic combination under those rules, and the variant is therefore classified as a variant of uncertain significance pending human review.3

PVS1 + PM2 VUS
1 vcep_p_v_s_1___d_e_c_i_s_i_o_n_t_r_e_e___p_t_e_n
3 generic_acmg_combination_rules
Gene diagram · NM_000314.8 · variants mapped to exon structure
PTEN NM_000314.8
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.
      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.
      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
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence
      COSMIC
      This variant has previously been reported in somatic cancers (COSMIC; COSV64292521, n = 2 times).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      Sources & reference links
      6Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB