chr6:31540071:G>A Detail (hg19) (LTA)

Information

Genome

Assembly Position
hg19 chr6:31,540,071-31,540,071
hg38 chr6:31,572,294-31,572,294 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000595.3:c.-162G>A
Ensemble ENST00000454783.5:c.-18G>A
ENST00000418386.3:c.-162G>A
Summary

MGeND

Clinical significance not provided
Variant entry
GWAS entry 1
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.394
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 153440 OMIM
HGNC 6709 HGNC
Ensembl ENSG00000226979 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24782563 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
not provided biliary cirrhosis, primary not provided MGS000089
(TMGS000168) 		Minoru Nakamura
Minoru Nakamura		 National Hospital Organization Nagasaki Medical Center
National Hospital Organization Nagasaki Medical Center
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.009 Fatigue Controlling for genomic estimates of ancestry and self-reported race/ethnicity a... BeFree 24632226 Detail
<0.001 Fatigue Controlling for genomic estimates of ancestry and self-reported race/ethnicity a... BeFree 24632226 Detail
0.002 Fatigue Controlling for genomic estimates of ancestry and self-reported race/ethnicity a... BeFree 24632226 Detail
Annotation

Annotations

DescrptionSourceLinks
Controlling for genomic estimates of ancestry and self-reported race/ethnicity and gender, the high ... DisGeNET Detail
Controlling for genomic estimates of ancestry and self-reported race/ethnicity and gender, the high ... DisGeNET Detail
Controlling for genomic estimates of ancestry and self-reported race/ethnicity and gender, the high ... 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
rs1800683 dbSNP
Genome
hg19
Position
chr6:31,540,071-31,540,071
Variant Type
snv
Reference Allele
G
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))
rs1800683
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3942
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6605
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
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