chr11:59863104:A>G Detail (hg19) (MS4A2)

Information

Genome

Assembly Position
hg19 chr11:59,863,104-59,863,104
hg38 chr11:60,095,631-60,095,631 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000139.4:c.710A>G NP_000130.1:p.Glu237Gly
NM_001256916.1:c.575A>G NP_001243845.1:p.Glu192Gly
Ensemble ENST00000278888.8:c.710A>G ENST00000278888.8:p.Glu237Gly
Summary

MGeND

Clinical significance Benign
Variant entry 0
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.127
ToMMo:0.148
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.172

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 147138 OMIM
HGNC 7316 HGNC
Ensembl ENSG00000149534 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv42709404 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2018/05/23 Aged, 100 and over germline MGS000013
(TMGS000027)
Hiroshi Mori Osaka City University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2001-09-01 no assertion criteria provided RECLASSIFIED - POLYMORPHISM germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Ischemic stroke In the non-hypertensive group, CCL11 rs3744508, LTC4S rs730012, FCER1B rs569108,... BeFree 22769019 Detail
<0.001 Ischemic Cerebrovascular Accident In the non-hypertensive group, CCL11 rs3744508, LTC4S rs730012, FCER1B rs569108,... BeFree 22769019 Detail
0.055 asthma To investigate whether the single-nucleotide polymorphisms (SNPs) Ile75Val and G... BeFree 22533235 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000139.5(MS4A2):c.710A>G (p.Glu237Gly) AND RECLASSIFIED - POLYMORPHISM ClinVar Detail
In the non-hypertensive group, CCL11 rs3744508, LTC4S rs730012, FCER1B rs569108, TGFB1 rs1800469, LT... DisGeNET Detail
In the non-hypertensive group, CCL11 rs3744508, LTC4S rs730012, FCER1B rs569108, TGFB1 rs1800469, LT... DisGeNET Detail
To investigate whether the single-nucleotide polymorphisms (SNPs) Ile75Val and Gln576Arg in the IL4R... 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
rs569108 dbSNP
Genome
hg19
Position
chr11:59,863,104-59,863,104
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1130
Mean of sample read depth (HGVD)
143.22
Standard deviation of sample read depth (HGVD)
66.70
Number of reference allele (HGVD)
1974
Number of alternative allele (HGVD)
286
Allele Frequency (HGVD)
0.12654867256637167
Gene Symbol (HGVD)
MS4A2
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))
rs569108
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.148
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2481
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
1483
East Asian Heterozygous Counts (ExAC)
1223
East Asian Homozygous Counts (ExAC)
130
East Asian Allele Frequency (ExAC)
0.1715640906987506
Chromosome Counts in All Race (ExAC)
121250
Allele Counts in All Race (ExAC)
5879
Heterozygous Counts in All Race (ExAC)
5155
Homozygous Counts in All Race (ExAC)
362
Allele Frequency in All Race (ExAC)
0.04848659793814433
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