chr5:56881616:G>A Detail (hg38) (MAP3K1)

Information

Genome

Assembly Position
hg19 chr5:56,177,443-56,177,443 View the variant detail on this assembly version.
hg38 chr5:56,881,616-56,881,616

HGVS

Type Transcript Protein
RefSeq NM_005921.1:c.2416G>A NP_005912.1:p.Asp806Asn
Ensemble ENST00000399503.4:c.2416G>A ENST00000399503.4:p.Asp806Asn
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.248
ToMMo:0.271
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.207

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600982 OMIM
HGNC 6848 HGNC
Ensembl ENSG00000095015 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21187344 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts 46,XY sex reversal 6 germline Detail
Benign 2018-11-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.001 Wheezing Interestingly, the study of gene-environment interactions showed that rhinovirus... BeFree 25326706 Detail
<0.001 Wheezing Interestingly, the study of gene-environment interactions showed that rhinovirus... BeFree 25326706 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_005921.2(MAP3K1):c.2416G>A (p.Asp806Asn) AND 46,XY sex reversal 6 ClinVar Detail
NM_005921.2(MAP3K1):c.2416G>A (p.Asp806Asn) AND not provided ClinVar Detail
Interestingly, the study of gene-environment interactions showed that rhinovirus was significantly a... DisGeNET Detail
Interestingly, the study of gene-environment interactions showed that rhinovirus was significantly a... DisGeNET 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
rs702689 dbSNP
Genome
hg38
Position
chr5:56,881,616-56,881,616
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
161.23
Standard deviation of sample read depth (HGVD)
69.77
Number of reference allele (HGVD)
1821
Number of alternative allele (HGVD)
599
Allele Frequency (HGVD)
0.24752066115702478
Gene Symbol (HGVD)
MAP3K1
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))
rs702689
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.271
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4542
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8612
East Asian Allele Counts (ExAC)
1779
East Asian Heterozygous Counts (ExAC)
1387
East Asian Homozygous Counts (ExAC)
196
East Asian Allele Frequency (ExAC)
0.206572224802601
Chromosome Counts in All Race (ExAC)
120648
Allele Counts in All Race (ExAC)
72190
Heterozygous Counts in All Race (ExAC)
25886
Homozygous Counts in All Race (ExAC)
23152
Allele Frequency in All Race (ExAC)
0.5983522312843976
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