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NTRK1
Final classification
VUS
PM2BP4
NTRK1
c.1334G>A
p.Arg445Lys
This variant

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

Transcript
NM_002529.3
HGVS · transcript:coding
NM_002529.3:c.1334G>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 applied · 11 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
NM_002529.3:c.1334G>A is absent from all population databases: gnomAD v2.1 (0 alleles), gnomAD v4.1 (0 alleles), and gnomAD-Canada v1.0 (0 alleles). The variant has a population allele frequency of 0.0, well below the PM2 threshold of <0.1%.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes)Absent from gnomAD-Canada v1.0 (genomes)
BP4 supporting Benign
Multiple lines of computational evidence predict no deleterious impact: REVEL score 0.277 (pathogenic threshold ≥0.5 not met), BayesDel score -0.176 (pathogenic threshold ≥0.27 not met), and SpliceAI max delta score 0.00 (no splicing impact predicted). All three in silico tools uniformly predict a benign effect.
REVEL: 0.277 (<0.5 threshold)BayesDel: -0.176 (<0.27 threshold)SpliceAI: max delta 0.00
Assessed · not applied · 4 not met · 7 not assessed
Pathogenic
PS3 OncoKB reports Unknown Oncogenic Effect for NTRK1 R445K with no variant-specific reviewed functional evidence.
PS4 This variant is absent from ClinVar and no case-control or cohort studies reporting this variant in affected individuals were identified.
PM1 The variant maps to codon 445 within the tyrosine kinase domain of NTRK1, and is absent from population databases (gnomAD).
PP2 NTRK1 is a disease gene for congenital insensitivity to pain with anhidrosis (CIPA), with missense variants reported as a known disease mechanism.
PP3 In silico tools uniformly predict a benign effect: REVEL score 0.277 (below the 0.5 threshold for pathogenicity), BayesDel score -0.176 (below the 0.27 threshold), and SpliceAI max delta score 0.00 (no predicted splice impact).
PP4 No patient phenotype or family history data are available for this case.
Benign
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS2 No observations of this variant in healthy adults have been reported.
BS3 No well-established in vitro or in vivo functional studies demonstrating no deleterious effect of NM_002529.3:c.1334G>A (p.Arg445Lys) were identified.
BP1 BP1 applies to missense variants in genes where only truncating variants cause disease.
N/A · 15 PVS1 · PS1 · PS2 · PM3 · PM4 · PM5 · PM6 · PP1 · PP5 · BS4 · BP2 · BP3 · BP5 · BP6 · BP7
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