chr5:131663062:T>C Detail (hg19) (SLC22A4, MIR3936HG)

Information

Genome

Assembly Position
hg19 chr5:131,663,062-131,663,062
hg38 chr5:132,327,369-132,327,369 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_003059.2:c.917T>C NP_003050.2:p.Ile306Thr
Ensemble ENST00000200652.4:c.917T>C ENST00000200652.4:p.Ile306Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.330
ToMMo:0.321
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.376

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 604190 OMIM
HGNC 10968 HGNC
Ensembl ENSG00000197208 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv22776818 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 not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.157 Inflammatory Bowel Diseases Polymorphisms R702W, G908R, and 3020insC of CARD15 (caspase activating recruitme... BeFree 17476680 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003059.3(SLC22A4):c.917T>C (p.Ile306Thr) AND not provided ClinVar Detail
Polymorphisms R702W, G908R, and 3020insC of CARD15 (caspase activating recruitment domain 15); Asp29... 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
rs272893 dbSNP
Genome
hg19
Position
chr5:131,663,062-131,663,062
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
62.96
Standard deviation of sample read depth (HGVD)
27.49
Number of reference allele (HGVD)
1619
Number of alternative allele (HGVD)
799
Allele Frequency (HGVD)
0.3304383788254756
Gene Symbol (HGVD)
SLC22A4
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))
rs272893
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3214
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5387
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
3245
East Asian Heterozygous Counts (ExAC)
2023
East Asian Homozygous Counts (ExAC)
611
East Asian Allele Frequency (ExAC)
0.3759267840593142
Chromosome Counts in All Race (ExAC)
121176
Allele Counts in All Race (ExAC)
69880
Heterozygous Counts in All Race (ExAC)
27810
Homozygous Counts in All Race (ExAC)
21035
Allele Frequency in All Race (ExAC)
0.5766818511916552
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