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NTRK1
Final classification
VUS
NTRK1 c.1334G>A · p.Arg445Lys
NTRK1

NM_002529.3:c.1334G>A (p.Arg445Lys) is a missense variant in exon 11 of NTRK1.

Gene
NTRK1
Transcript
NM_002529.3
HGVS · transcript:coding
NM_002529.3:c.1334G>A
Consequence
N/A
GRCh38
chr1:156874988 G>A
GRCh37
chr1:156844780 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 moderate, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, 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, BP4 supporting benign; combination = 1 moderate + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
NTRK1 c.1334G>A

NM_002529.3:c.1334G>A (p.Arg445Lys) is a missense variant in exon 11 of NTRK1. This variant is absent from all population databases: gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency 0.0; PM2 met at moderate strength).1 Multiple lines of computational evidence predict a benign effect: REVEL 0.277, BayesDel -0.176, SpliceAI max delta 0.00 (BP4 met at supporting benign strength).2 No published literature, ClinVar submissions, or functional studies specific to this variant were identified.3 NTRK1 loss-of-function variants cause autosomal recessive congenital insensitivity to pain with anhidrosis (CIPA); missense variants are a known disease mechanism. Applying generic ACMG/AMP 2015 final classification rules (PMID:25741868): one moderate pathogenic criterion (PM2) and one supporting benign criterion (BP4) are insufficient to classify as likely pathogenic or likely benign. The variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 generic_acmg_combination_rules
Gene diagram · NM_002529.3 · variants mapped to exon structure
NTRK1 NM_002529.3
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.
      🇨🇦 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 = 0.277. BayesDel score = -0.176181.
      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. NTRK1, a receptor tyrosine kinase, is altered by gene fusions 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