chr1:156873600:T>A Detail (hg38) (NTRK1)

Information

Genome

Assembly Position
hg19 chr1:156,843,392-156,843,392 View the variant detail on this assembly version.
hg38 chr1:156,873,600-156,873,600

HGVS

Type Transcript Protein
RefSeq NM_002529.3:c.851-33T>A
NM_001012331.1:c.851-33T>A
NM_001007792.1:c.689-33T>A
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 191315 OMIM
HGNC 8031 HGNC
Ensembl ENSG00000198400 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv3389836 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other germline MGS000073
(TMGS000185) 		Kenjiro Kosaki
 Keio University
IRUD
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2024-01-17 criteria provided, multiple submitters, no conflicts Hereditary insensitivity to pain with anhidrosis germline paternal Detail
Pathogenic 2014-01-21 criteria provided, single submitter Inborn genetic diseases germline Detail
Pathogenic 2022-12-14 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.450 HSAN Type IV NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002529.4(NTRK1):c.851-33T>A AND Hereditary insensitivity to pain with anhidrosis ClinVar Detail
NM_002529.4(NTRK1):c.851-33T>A AND Inborn genetic diseases ClinVar Detail
NM_002529.4(NTRK1):c.851-33T>A AND not provided ClinVar Detail
NA DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs80356674 dbSNP
Genome
hg38
Position
chr1:156,873,600-156,873,600
Variant Type
snv
Reference Allele
T
Alternative Allele
A
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs80356674
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
6764
East Asian Allele Counts (ExAC)
3
East Asian Heterozygous Counts (ExAC)
3
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
4.435245416913069E-4
Chromosome Counts in All Race (ExAC)
89436
Allele Counts in All Race (ExAC)
3
Heterozygous Counts in All Race (ExAC)
3
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
3.354353951428955E-5
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