chr17:76867017:C>T Detail (hg19) (TIMP2)

Information

Genome

Assembly Position
hg19 chr17:76,867,017-76,867,017
hg38 chr17:78,870,935-78,870,935 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_003255.4:c.303G>A NP_003246.1:p.Ser101=
Ensemble ENST00000586057.5:c.72G>A ENST00000586057.5:p.Ser24=
ENST00000586713.6:c.72G>A ENST00000586713.6:p.Ser24=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.139
ToMMo:0.128
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.226

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 188825 OMIM
HGNC 11821 HGNC
Ensembl ENSG00000035862 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv58818135 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-06-11 criteria provided, single submitter TIMP2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Thickening of pleura The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs... BeFree 24142982 Detail
<0.001 Thickening of pleura The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs... BeFree 24142982 Detail
<0.001 Thickening of pleura The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs... BeFree 24142982 Detail
<0.001 pulmonary emphysema The TIMP2 rs2277698 SNP was associated with overall (p = 0.022) and paraseptal (... BeFree 23734748 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003255.5(TIMP2):c.303G>A (p.Ser101=) AND TIMP2-related disorder ClinVar Detail
The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs1800470 SNPs were as... DisGeNET Detail
The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs1800470 SNPs were as... DisGeNET Detail
The TIMP2 rs2277698 SNP and a haplotype consisting of the TGFB1 rs1800469 and rs1800470 SNPs were as... DisGeNET Detail
The TIMP2 rs2277698 SNP was associated with overall (p = 0.022) and paraseptal (p = 0.010) emphysema... 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
chr17:76,867,017-76,867,017
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
177.51
Standard deviation of sample read depth (HGVD)
80.57
Number of reference allele (HGVD)
2083
Number of alternative allele (HGVD)
337
Allele Frequency (HGVD)
0.13925619834710745
Gene Symbol (HGVD)
TIMP2
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))
rs2277698
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1277
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2140
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)
1959
East Asian Heterozygous Counts (ExAC)
1491
East Asian Homozygous Counts (ExAC)
234
East Asian Allele Frequency (ExAC)
0.22647398843930636
Chromosome Counts in All Race (ExAC)
121312
Allele Counts in All Race (ExAC)
16770
Heterozygous Counts in All Race (ExAC)
14036
Homozygous Counts in All Race (ExAC)
1367
Allele Frequency in All Race (ExAC)
0.13823859140068584
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