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NTRK2
Final classification
VUS
NTRK2 c.2061C>A · p.His687Gln
NTRK2

NM_006180.4:c.2061C>A (p.His687Gln) is a missense variant in exon 19 of NTRK2. It is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada), meeting PM2.

Gene
NTRK2
Transcript
NM_006180.4
HGVS · transcript:coding
NM_006180.4:c.2061C>A
Consequence
N/A
GRCh38
chr9:84955406 C>A
GRCh37
chr9:87570321 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: PM2 moderate; combination = 1 moderate, 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; combination = 1 moderate, which maps to VUS.
Classification rationale
PM2 VUS
NTRK2 c.2061C>A

NM_006180.4:c.2061C>A (p.His687Gln) is a missense variant in exon 19 of NTRK2. It is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada), meeting PM2.1 No functional studies, case reports, segregation data, de novo observations, or ClinVar classifications are available for this variant. No publications specifically mention NM_006180.4:c.2061C>A.2 Computational predictors are discordant: REVEL score 0.77 supports a deleterious effect, but BayesDel score 0.307 is borderline and does not provide a second concordant predictor to meet PP3. SpliceAI predicts no splicing impact (max delta = 0.00).3 With only PM2 (moderate) met, the evidence is insufficient to classify this variant as likely pathogenic or pathogenic under the ACMG/AMP 2015 framework (PMID:25741868). The variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 VUS
3 revelbayesdelspliceai ↗
4 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 · 1 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 = 0.77. BayesDel score = 0.307499.
      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. NTRK2, a receptor tyrosine kinase, is altered by mutation or chromosomal rearrangement in a diverse range of cancers.
      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