Starting
Initialising…
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NTRK1
Final classification
VUS
NTRK1 c.1065C>A · p.Asn355Lys
NTRK1

NM_002529.3:c.1065C>A (p.Asn355Lys) is a missense variant in NTRK1, a gene in which loss-of-function variants cause autosomal recessive congenital insensitivity to pain with anhidrosis (CIPA).

Gene
NTRK1
Transcript
NM_002529.3
HGVS · transcript:coding
NM_002529.3:c.1065C>A
Consequence
N/A
GRCh38
chr1:156873847 C>A
GRCh37
chr1:156843639 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
NTRK1 c.1065C>A

NM_002529.3:c.1065C>A (p.Asn355Lys) is a missense variant in NTRK1, a gene in which loss-of-function variants cause autosomal recessive congenital insensitivity to pain with anhidrosis (CIPA).1 This variant is absent from large population databases (gnomAD v2.1 and v4.1), supporting PM2 at moderate strength.2 In silico predictors are inconclusive: REVEL score is 0.372 (intermediate, not reaching pathogenic thresholds) and BayesDel is -0.315 (benign-leaning). SpliceAI predicts no splicing impact (max delta = 0.00). PP3 and BP4 are not met.3 No functional studies, de novo reports, cosegregation data, or ClinVar submissions were identified for this variant. PVS1 does not apply as the variant is a missense substitution, not a null variant.4 Only PM2 (moderate) is met. Under generic ACMG/AMP 2015 combination rules (PMID:25741868), a single moderate criterion is insufficient to reach Likely Pathogenic or Likely Benign. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 VUS
1 pvs1_gene_context
3 revelbayesdelspliceai ↗
4 pvs1_variant_assessmentclinvar ↗oncokb ↗
5 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 · 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
      Population frequency
      Absent from gnomAD v4.1.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      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 = 0.372. BayesDel score = -0.315045.
      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
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots