chr22:42276742:G>C Detail (hg19) (SREBF2)

Information

Genome

Assembly Position
hg19 chr22:42,276,742-42,276,742
hg38 chr22:41,880,738-41,880,738 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_004599.3:c.1784G>C NP_004590.2:p.Gly595Ala
Ensemble ENST00000361204.9:c.1784G>C ENST00000361204.9:p.Gly595Ala
ENST00000710853.1:c.1694G>C ENST00000710853.1:p.Gly565Ala
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.339
ToMMo:0.344
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.179

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600481 OMIM
HGNC 11290 HGNC
Ensembl ENSG00000198911 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv66040714 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-05-04 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.003 myocardial infarction SREBF-2 1784G > C single nucleotide polymorphism (SNP, rs2228314) and SCAP 23... BeFree 20111910 Detail
0.002 Non-alcoholic Fatty Liver Disease Relationship of SREBP-2 rs2228314 G>C polymorphism with nonalcoholic fatty li... BeFree 24992162 Detail
0.002 Non-alcoholic Fatty Liver Disease SREBP-2 1784 G/C genotype is associated with non-alcoholic fatty liver disease i... BeFree 22182810 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004599.4(SREBF2):c.1784G>C (p.Gly595Ala) AND not provided ClinVar Detail
SREBF-2 1784G > C single nucleotide polymorphism (SNP, rs2228314) and SCAP 2386A > G variant (... DisGeNET Detail
Relationship of SREBP-2 rs2228314 G>C polymorphism with nonalcoholic fatty liver disease in a Han... DisGeNET Detail
SREBP-2 1784 G/C genotype is associated with non-alcoholic fatty liver disease in north Indians. 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
rs2228314 dbSNP
Genome
hg19
Position
chr22:42,276,742-42,276,742
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1186
Mean of sample read depth (HGVD)
63.49
Standard deviation of sample read depth (HGVD)
31.80
Number of reference allele (HGVD)
1567
Number of alternative allele (HGVD)
805
Allele Frequency (HGVD)
0.3393760539629005
Gene Symbol (HGVD)
SREBF2
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))
rs2228314
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3436
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5759
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8628
East Asian Allele Counts (ExAC)
1548
East Asian Heterozygous Counts (ExAC)
1246
East Asian Homozygous Counts (ExAC)
151
East Asian Allele Frequency (ExAC)
0.17941585535465926
Chromosome Counts in All Race (ExAC)
121106
Allele Counts in All Race (ExAC)
40434
Heterozygous Counts in All Race (ExAC)
23662
Homozygous Counts in All Race (ExAC)
8386
Allele Frequency in All Race (ExAC)
0.333872805641339
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