chr17:32583269:T>C Detail (hg19) (CCL2)

Information

Genome

Assembly Position
hg19 chr17:32,583,269-32,583,269
hg38 chr17:34,256,250-34,256,250 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_002982.3:c.105T>C NP_002973.1:p.Cys35=
Ensemble ENST00000225831.4:c.105T>C ENST00000225831.4:p.Cys35=
ENST00000580907.6:c.105T>C ENST00000580907.6:p.Cys35=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.654
ToMMo:0.663
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.563

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 158105 OMIM
HGNC 10618 HGNC
Ensembl ENSG00000108691 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57566107 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-10-17 criteria provided, single submitter CCL2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 kidney failure Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 ... BeFree 22817530 Detail
<0.001 Kidney Failure, Chronic Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 ... BeFree 22817530 Detail
0.207 Kidney Failure, Chronic Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 ... BeFree 22817530 Detail
0.002 kidney failure Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 ... BeFree 22817530 Detail
0.480 age related macular degeneration The binary logistic regression model is an appropriate tool to predict AMD in th... BeFree 23848218 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002982.4(CCL2):c.105T>C (p.Cys35=) AND CCL2-related disorder ClinVar Detail
Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 receptor (IL4R) gene... DisGeNET Detail
Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 receptor (IL4R) gene... DisGeNET Detail
Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 receptor (IL4R) gene... DisGeNET Detail
Four polymorphisms showed association with ESRD: rs1801275 in the interleukin 4 receptor (IL4R) gene... DisGeNET Detail
The binary logistic regression model is an appropriate tool to predict AMD in the presence of serum ... 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
-
Genome
hg19
Position
chr17:32,583,269-32,583,269
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1203
Mean of sample read depth (HGVD)
59.42
Standard deviation of sample read depth (HGVD)
30.54
Number of reference allele (HGVD)
832
Number of alternative allele (HGVD)
1571
Allele Frequency (HGVD)
0.653766125676238
Gene Symbol (HGVD)
CCL2
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))
rs4586
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6632
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11115
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
4863
East Asian Heterozygous Counts (ExAC)
2089
East Asian Homozygous Counts (ExAC)
1387
East Asian Allele Frequency (ExAC)
0.5627169636658181
Chromosome Counts in All Race (ExAC)
121352
Allele Counts in All Race (ExAC)
53639
Heterozygous Counts in All Race (ExAC)
28203
Homozygous Counts in All Race (ExAC)
12718
Allele Frequency in All Race (ExAC)
0.4420116685345112
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