chr1:156815825:G>A Detail (hg38) (NTRK1, SH2D2A)

Information

Genome

Assembly Position
hg19 chr1:156,785,617-156,785,617 View the variant detail on this assembly version.
hg38 chr1:156,815,825-156,815,825

HGVS

Type Transcript Protein
RefSeq NM_001007792.1:c.-77G>A
Ensemble ENST00000392302.7:c.-77G>A
ENST00000674537.2:c.-217G>A
Type Transcript Protein
RefSeq NM_001161442.1:c.69+181C>T
NM_001161443.1:c.69+181C>T
NM_001161444.1:c.123+181C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.817
ToMMo:0.814
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.822

Prediction

ClinVar

Clinical Significance Benign
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 tgv3386857 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 604514 OMIM
HGNC 10821 HGNC
Ensembl ENSG00000027869 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv3386857 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-01-07 criteria provided, single submitter not specified germline Detail
Benign 2021-07-08 criteria provided, single submitter Hereditary insensitivity to pain with anhidrosis germline Detail
Benign 2023-07-07 criteria provided, single submitter X-linked lymphoproliferative disease due to SH2D1A deficiency germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_003975.4(SH2D2A):c.123+181C>T AND not specified ClinVar Detail
NM_003975.4(SH2D2A):c.123+181C>T AND Hereditary insensitivity to pain with anhidrosis ClinVar Detail
NM_003975.4(SH2D2A):c.123+181C>T AND X-linked lymphoproliferative disease due to SH2D1A deficiency ClinVar Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1800601 dbSNP
Genome
hg38
Position
chr1:156,815,825-156,815,825
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
148.02
Standard deviation of sample read depth (HGVD)
61.32
Number of reference allele (HGVD)
444
Number of alternative allele (HGVD)
1976
Allele Frequency (HGVD)
0.8165289256198347
Gene Symbol (HGVD)
NTRK1
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))
rs1800601
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.8145
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
13651
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
7109
East Asian Heterozygous Counts (ExAC)
1255
East Asian Homozygous Counts (ExAC)
2927
East Asian Allele Frequency (ExAC)
0.8218497109826589
Chromosome Counts in All Race (ExAC)
121290
Allele Counts in All Race (ExAC)
80950
Heterozygous Counts in All Race (ExAC)
26138
Homozygous Counts in All Race (ExAC)
27406
Allele Frequency in All Race (ExAC)
0.6674086899167285
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