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NTRK2
Final classification
VUS
NTRK2 c.2033C>T · p.Ala678Val
NTRK2

NM_006180.4:c.2033C>T (p.Ala678Val) in NTRK2 is a missense variant for which no CSPEC or VCEP gene-specific framework is available; classification proceeds under generic ACMG/AMP 2015 guidelines.

Gene
NTRK2
Transcript
NM_006180.4
HGVS · transcript:coding
NM_006180.4:c.2033C>T
Consequence
N/A
GRCh38
chr9:84955378 C>T
GRCh37
chr9:87570293 C>T
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 supporting; combination = 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 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
NTRK2 c.2033C>T

NM_006180.4:c.2033C>T (p.Ala678Val) in NTRK2 is a missense variant for which no CSPEC or VCEP gene-specific framework is available; classification proceeds under generic ACMG/AMP 2015 guidelines.1 This variant is absent from gnomAD v2.1 and gnomAD-Canada, and is present at an extremely low frequency in gnomAD v4.1 (4/1,613,948 alleles, AF = 2.48e-06, 0.00025%), meeting PM2 at supporting strength.2 No pathogenic or benign criteria beyond PM2_supporting were met. PVS1/BP7 are not applicable to this missense variant. In silico predictors are discordant (REVEL 0.654 damaging, BayesDel 0.073 benign, SpliceAI delta 0.00), so PP3 and BP4 are not met. No functional studies, segregation data, de novo reports, or hotspot evidence were available.3 The variant is reported in ClinVar (Variation ID 1393489) as Uncertain significance by a single clinical laboratory (Labcorp Genetics, SCV002166224), consistent with the limited evidence available for classification.4 With only one supporting pathogenic criterion (PM2) met and no benign criteria met, this variant is classified as a Variant of Uncertain Significance (VUS) under the generic ACMG/AMP 2015 framework.5

PM2 VUS
1 generic_acmg_combination_rules
3 revelbayesdelspliceai ↗oncokb ↗
5 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
      This variant is present in gnomAD v4.1 (AF= 2.47839e-06; MAF= 0.00025%, 4/1613948 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 3.37815e-05; MAF= 0.00338%, 1/29602 alleles, homozygotes = 0); grpmax FAF= 2.8e-07.
      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
      0.00025% · 4 / 1,613,948
      0 hom · FAF 2.8e-05%
      Ashkenazi Jewish
      1 / 29,602
      0.0034%
      East Asian
      1 / 44,888
      0.0022%
      European (non-Finnish)
      2 / 1,179,956
      0.00017%
      + 7 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, African/African American)
      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 has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 1393489)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.654. BayesDel score = 0.072725.
      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 previously been reported in somatic cancers (COSMIC; COSV52875759, n = 1 times).
      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