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NTRK1
Final classification
VUS
NTRK1 c.737C>T · p.Ser246Phe
NTRK1

NM_002529.3:c.737C>T (p.Ser246Phe) is a missense variant in NTRK1, a gene associated with autosomal recessive congenital insensitivity to pain with anhidrosis (CIPA).

Gene
NTRK1
Transcript
NM_002529.3
HGVS · transcript:coding
NM_002529.3:c.737C>T
Consequence
N/A
GRCh38
chr1:156871642 C>T
GRCh37
chr1:156841434 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 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.737C>T

NM_002529.3:c.737C>T (p.Ser246Phe) is a missense variant in NTRK1, a gene associated with autosomal recessive congenital insensitivity to pain with anhidrosis (CIPA). This variant is absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (1/1,614,010 alleles; overall AF=6.20×10⁻⁷; highest subpopulation AF=1.10×10⁻⁵ in South Asian), satisfying PM2 at moderate strength.1 Multiple in silico tools predict a benign effect: REVEL score of 0.132, BayesDel score of -0.415, and SpliceAI max delta of 0.01. These support BP4 at supporting benign strength.2 This missense variant is not eligible for PVS1 as it does not fall into the null-variant buckets of nonsense, frameshift, or canonical splice site variants per ClinGen SVI PVS1 recommendations (PMC6185798).3 No functional studies, de novo reports, segregation data, case-control data, or ClinVar classifications exist for this variant. No publications mention NM_002529.3:c.737C>T. The evidence profile consists of PM2 (moderate) and BP4 (supporting benign). Under generic ACMG/AMP 2015 combination rules, this combination does not meet the threshold for pathogenic, likely pathogenic, benign, or likely benign classification, and the variant therefore remains 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 · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 moderate Pathogenic
NM_002529.3:c.737C>T is absent from gnomAD v2.1 and is present at extremely low frequency in gnomAD v4.1 (1/1,614,010 alleles, overall AF=6.20×10⁻⁷; highest subpopulation AF=1.10×10⁻⁵ in South Asian, 1/91,076 alleles). The total population allele frequency is well below the 0.1% threshold for PM2 in a non-VCEP framework.
gnoMAD v2.1: absent. gnomAD v4.1: 1/1614010 alleles (AF=6.20×10⁻⁷
BP4 supporting Benign
Multiple lines of computational evidence suggest p.(Ser246Phe) does not have a deleterious effect. REVEL score is 0.132 (below the 0.5 pathogenic threshold), BayesDel score is -0.415 (consistent with a benign prediction), and SpliceAI max delta score is 0.01 (no predicted splicing impact). All available in silico tools are concordant in predicting a non-damaging effect.
REVEL: 0.132. BayesDel: -0.415. SpliceAI: 0.01. All in silico tools predict a benign/neutral effect.
Assessed · not applied
Pathogenic
PS1 No alternate nucleotide change at codon 737 resulting in the same p.(Ser246Phe) amino acid change has been established as pathogenic.
PS2 No de novo observation has been reported for NM_002529.3:c.737C>T.
PS3 No functional studies have been identified for p.(Ser246Phe) or for a systematically characterized range that includes residue 246.
PS4 This variant is absent from ClinVar and no affected individuals have been reported in the literature with NM_002529.3:c.737C>T.
PM1 Residue 246 in NTRK1 is not located in a statistically significant mutational hotspot per cancerhotspots.org.
PM6 No de novo observation has been reported for NM_002529.3:c.737C>T in any publication or database.
PP1 No co-segregation data are available for NM_002529.3:c.737C>T.
PP2 NTRK1 is associated with CIPA (congenital insensitivity to pain with anhidrosis), an autosomal recessive disorder, and loss-of-function missense variants are a recognized disease mechanism.
PP3 Multiple in silico tools do not support a deleterious effect for p.(Ser246Phe).
PP4 No patient phenotype or clinical data are available for NM_002529.3:c.737C>T.
PP5 NM_002529.3:c.737C>T is absent from ClinVar and has not been reported as pathogenic by any reputable source.
Benign
BA1 The allele frequency of NM_002529.3:c.737C>T in gnomAD v4.1 is 6.20×10⁻⁷ (0.000062%), far below the 1% non-VCEP BA1 threshold.
BS1 The allele frequency of NM_002529.3:c.737C>T is 6.20×10⁻⁷ (0.000062%), far below the 0.3% non-VCEP BS1 threshold.
BS2 No homozygous individuals have been observed in gnomAD v2.1 or v4.1 for NM_002529.3:c.737C>T.
BS3 No well-established functional studies demonstrate a neutral or non-damaging effect for p.(Ser246Phe).
BS4 No segregation data are available for NM_002529.3:c.737C>T.
BP1 NTRK1 is associated with CIPA, and both missense and truncating variants are established disease mechanisms.
BP2 BP2 applies to observation in trans with a pathogenic variant in a fully penetrant dominant disorder.
BP5 No case has been reported in which NM_002529.3:c.737C>T was found in an individual with an alternate molecular basis for disease.
BP6 NM_002529.3:c.737C>T is absent from ClinVar and has not been reported as benign by any reputable source.
N/A · 3 PVS1 · PM5 · BP7
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= 6.19575e-07; MAF= 0.00006%, 1/1614010 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 1.09798e-05; MAF= 0.00110%, 1/91076 alleles, homozygotes = 0).
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
6.2e-05% · 1 / 1,614,010
0 hom
South Asian
1 / 91,076
0.0011%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, African/African American, European (non-Finnish))
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 = 0.01). REVEL score = 0.132. BayesDel score = -0.415422.
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 previously been reported in somatic cancers (COSMIC; COSV62325297, 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