Starting
Initialising…
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NTRK3
Final classification
VUS
NTRK3 c.428C>T · p.Ser143Leu
NTRK3

NM_001012338.2:c.428C>T is a missense variant in NTRK3 resulting in a serine to leucine substitution at codon 143 (p.Ser143Leu).

Gene
NTRK3
Transcript
NM_001012338.2
HGVS · transcript:coding
NM_001012338.2:c.428C>T
Consequence
N/A
GRCh38
chr15:88147371 G>A
GRCh37
chr15:88690602 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 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
NTRK3 c.428C>T

NM_001012338.2:c.428C>T is a missense variant in NTRK3 resulting in a serine to leucine substitution at codon 143 (p.Ser143Leu). This variant is present at extremely low frequency in gnomAD population databases (v2.1 AF=7.96×10⁻⁶, 2/251,180 alleles; v4.1 AF=4.96×10⁻⁶, 8/1,613,870 alleles; no homozygotes; grpmax FAF=2.93×10⁻⁶), meeting PM2 at supporting strength.1 The variant is absent from ClinVar and has not been reported in the germline literature. It is also absent from COSMIC (somatic cancer database) and OncoKB assigns an Unknown Oncogenic Effect classification.2 In silico predictors are equivocal: REVEL score is 0.491 (borderline, below the 0.5 damaging threshold), BayesDel is 0.215, and SpliceAI predicts no splicing impact (max delta 0.03). Neither PP3 nor BP4 is met.3 No functional studies, segregation data, de novo observations, or case-control data are available for this variant. The residue Ser143 is not located in a known mutational hotspot. No CSPEC or VCEP framework exists for NTRK3. Applying generic ACMG/AMP 2015 rules, the only applicable criterion is PM2 (supporting). This is insufficient to classify the variant as likely pathogenic or likely benign.4 Overall, NM_001012338.2:c.428C>T is classified as a Variant of Uncertain Significance (VUS) based on a single supporting pathogenic criterion (PM2) and no applicable benign criteria.

PM2 VUS
3 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_001012338.2 · variants mapped to exon structure
NTRK3 NM_001012338.2
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= 4.95703e-06; MAF= 0.00050%, 8/1613870 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.78079e-06; MAF= 0.00068%, 8/1179804 alleles, homozygotes = 0); grpmax FAF= 2.92e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 7.96242e-06; MAF= 0.00080%, 2/251180 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.7614e-05; MAF= 0.00176%, 2/113546 alleles, homozygotes = 0); grpmax FAF= 2.93e-06.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0005% · 8 / 1,613,870
      0 hom · FAF 0.00029%
      European (non-Finnish)
      8 / 1,179,804
      0.00068%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0008% · 2 / 251,180
      0 hom · FAF 0.00029%
      European (non-Finnish)
      2 / 113,546
      0.0018%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      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 = 0.03). REVEL score = 0.491. BayesDel score = 0.214812.
      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. NTRK3, a receptor tyrosine kinase, is altered by gene fusion 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