1-156881634-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_002529.4(NTRK1):c.2383C>T(p.Leu795Leu) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000413 in 1,453,714 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
NTRK1
NM_002529.4 synonymous
NM_002529.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.16
Publications
0 publications found
Genes affected
NTRK1 (HGNC:8031): (neurotrophic receptor tyrosine kinase 1) This gene encodes a member of the neurotrophic tyrosine kinase receptor (NTKR) family. This kinase is a membrane-bound receptor that, upon neurotrophin binding, phosphorylates itself and members of the MAPK pathway. The presence of this kinase leads to cell differentiation and may play a role in specifying sensory neuron subtypes. Mutations in this gene have been associated with congenital insensitivity to pain, anhidrosis, self-mutilating behavior, cognitive disability and cancer. Alternate transcriptional splice variants of this gene have been found, but only three have been characterized to date. [provided by RefSeq, Jul 2008]
NTRK1 Gene-Disease associations (from GenCC):
- hereditary sensory and autonomic neuropathy type 4Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, ClinGen, Labcorp Genetics (formerly Invitae)
- familial medullary thyroid carcinomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 1-156881634-C-T is Benign according to our data. Variant chr1-156881634-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 741663.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTRK1 | NM_002529.4 | c.2383C>T | p.Leu795Leu | synonymous_variant | Exon 17 of 17 | ENST00000524377.7 | NP_002520.2 | |
NTRK1 | NM_001012331.2 | c.2365C>T | p.Leu789Leu | synonymous_variant | Exon 16 of 16 | NP_001012331.1 | ||
NTRK1 | NM_001007792.1 | c.2275C>T | p.Leu759Leu | synonymous_variant | Exon 17 of 17 | NP_001007793.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.0000130 AC: 3AN: 231442 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
3
AN:
231442
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1453714Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 722452 show subpopulations
GnomAD4 exome
AF:
AC:
6
AN:
1453714
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
722452
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33324
American (AMR)
AF:
AC:
2
AN:
43738
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25884
East Asian (EAS)
AF:
AC:
0
AN:
39404
South Asian (SAS)
AF:
AC:
1
AN:
84804
European-Finnish (FIN)
AF:
AC:
0
AN:
52174
Middle Eastern (MID)
AF:
AC:
0
AN:
5460
European-Non Finnish (NFE)
AF:
AC:
3
AN:
1108974
Other (OTH)
AF:
AC:
0
AN:
59952
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.542
Heterozygous variant carriers
0
1
1
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0.00
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 25, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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