chr2:136873084:G>A Detail (hg19) (CXCR4)

Information

Genome

Assembly Position
hg19 chr2:136,873,084-136,873,084
hg38 chr2:136,115,514-136,115,514 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_003467.2:c.414C>T NP_003458.1:p.Ile138=
NM_001008540.1:c.426C>T NP_001008540.1:p.Ile142=
Ensemble ENST00000241393.4:c.414C>T ENST00000241393.4:p.Ile138=
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.088
ToMMo:0.071
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.120

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 162643 OMIM
HGNC 2561 HGNC
Ensembl ENSG00000121966 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv8733491 TogoVar
COSMIC COSM148942 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign criteria provided, single submitter not specified germline Detail
Benign 2024-02-01 criteria provided, single submitter Warts, hypogammaglobulinemia, infections, and myelokathexis germline Detail
Benign 2020-10-06 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.029 Malignant neoplasm of breast Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... BeFree 19196101 Detail
0.006 Malignant neoplasm of breast Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... BeFree 19196101 Detail
0.004 breast carcinoma Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... BeFree 19196101 Detail
0.026 breast carcinoma Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... BeFree 19196101 Detail
0.065 breast carcinoma Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... BeFree 19196101 Detail
0.105 Malignant neoplasm of breast Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) an... BeFree 19196101 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003467.3(CXCR4):c.414C>T (p.Ile138=) AND not specified ClinVar Detail
NM_003467.3(CXCR4):c.414C>T (p.Ile138=) AND Warts, hypogammaglobulinemia, infections, and myelokathe... ClinVar Detail
NM_003467.3(CXCR4):c.414C>T (p.Ile138=) AND not provided ClinVar Detail
Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... DisGeNET Detail
Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... DisGeNET Detail
Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... DisGeNET Detail
Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... DisGeNET Detail
Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... DisGeNET Detail
Similarly, the SNP barcode of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-VEGF) and rs12812942-rs31366... 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
rs2228014 dbSNP
Genome
hg19
Position
chr2:136,873,084-136,873,084
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
156.55
Standard deviation of sample read depth (HGVD)
73.87
Number of reference allele (HGVD)
2206
Number of alternative allele (HGVD)
214
Allele Frequency (HGVD)
0.0884297520661157
Gene Symbol (HGVD)
CXCR4
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))
rs2228014
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0707
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1185
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
1042
East Asian Heterozygous Counts (ExAC)
914
East Asian Homozygous Counts (ExAC)
64
East Asian Allele Frequency (ExAC)
0.12046242774566474
Chromosome Counts in All Race (ExAC)
121396
Allele Counts in All Race (ExAC)
5583
Heterozygous Counts in All Race (ExAC)
5173
Homozygous Counts in All Race (ExAC)
205
Allele Frequency in All Race (ExAC)
0.04598998319549244
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