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NTRK2
Final classification
Likely Pathogenic
NTRK2 c.1529C>A · p.Ser510Ter
NTRK2

NM_006180.4:c.1529C>A is a nonsense variant in NTRK2 predicting p.(Ser510Ter), meeting PVS1 at very strong strength under the ClinGen SVI PVS1 framework (PMC6185798). NTRK2 loss-of-function is an established mechanism for autosomal dominant obesity, hyperphagia, and developmental delay (MIM #613886). The premature termination codon in exon 16 of 20 is predicted to trigger nonsense-mediated decay.

Gene
NTRK2
Transcript
NM_006180.4
HGVS · transcript:coding
NM_006180.4:c.1529C>A
Consequence
N/A
GRCh38
chr9:84867327 C>A
GRCh37
chr9:87482242 C>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 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
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 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
NTRK2 c.1529C>A

NM_006180.4:c.1529C>A is a nonsense variant in NTRK2 predicting p.(Ser510Ter), meeting PVS1 at very strong strength under the ClinGen SVI PVS1 framework (PMC6185798). NTRK2 loss-of-function is an established mechanism for autosomal dominant obesity, hyperphagia, and developmental delay (MIM #613886). The premature termination codon in exon 16 of 20 is predicted to trigger nonsense-mediated decay.1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, meeting PM2 at moderate strength.2 Applying generic ACMG/AMP 2015 combination rules (PMID:25741868): one Very Strong criterion (PVS1) plus one Moderate criterion (PM2) meets the threshold for Pathogenic classification.3 The pipeline-derived PVS1 gene-context literature search returned five supporting papers (PMIDs 42018264, 30717682, 32082673, 39112663, 39341363), but none of these papers mention NM_006180.4:c.1529C>A or provide evidence for NTRK2 germline loss-of-function as a disease mechanism. The gene-level PVS1 eligibility determination is independently supported by established OMIM curation (MIM #613886) rather than by the pipeline's literature search results.

PVS1 + PM2 Likely Pathogenic
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
3 generic_acmg_combination_rules
Gene diagram · NM_006180.4 · variants mapped to exon structure
NTRK2 NM_006180.4
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 · supports pathogenic
      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 = 0.19). BayesDel score = 0.66.
      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