chr15:45554267:C>A Detail (hg19) (SLC28A2, SLC28A2-AS1)

Information

Genome

Assembly Position
hg19 chr15:45,554,267-45,554,267
hg38 chr15:45,262,069-45,262,069 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_004212.3:c.225C>A NP_004203.2:p.Ser75Arg
Ensemble ENST00000347644.8:c.225C>A ENST00000347644.8:p.Ser75Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.056
ToMMo:0.056
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.083

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 606208 OMIM
HGNC 11002 HGNC
Ensembl ENSG00000137860 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv52798017 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-01-18 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 cryoglobulinemia Non response was negatively predicted by cryoglobulinemia and IL28B_rs12980275 A... BeFree 25661337 Detail
<0.001 cryoglobulinemia Non response was negatively predicted by cryoglobulinemia and IL28B_rs12980275 A... BeFree 25661337 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004212.4(SLC28A2):c.225C>A (p.Ser75Arg) AND not provided ClinVar Detail
Non response was negatively predicted by cryoglobulinemia and IL28B_rs12980275 AA genotype and posit... DisGeNET Detail
Non response was negatively predicted by cryoglobulinemia and IL28B_rs12980275 AA genotype and posit... 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
rs1060896 dbSNP
Genome
hg19
Position
chr15:45,554,267-45,554,267
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
54.98
Standard deviation of sample read depth (HGVD)
30.82
Number of reference allele (HGVD)
2283
Number of alternative allele (HGVD)
135
Allele Frequency (HGVD)
0.05583126550868486
Gene Symbol (HGVD)
SLC28A2
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))
rs1060896
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0557
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
934
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
722
East Asian Heterozygous Counts (ExAC)
636
East Asian Homozygous Counts (ExAC)
43
East Asian Allele Frequency (ExAC)
0.08344891354600092
Chromosome Counts in All Race (ExAC)
121362
Allele Counts in All Race (ExAC)
60904
Heterozygous Counts in All Race (ExAC)
25474
Homozygous Counts in All Race (ExAC)
17715
Allele Frequency in All Race (ExAC)
0.5018374779585043
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