chrX:47444985:T>C Detail (hg19) (SYN1, TIMP1)

Information

Genome

Assembly Position
hg19 chrX:47,444,985-47,444,985
hg38 chrX:47,585,586-47,585,586 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_006950.3:c.775-8085A>G
NM_133499.2:c.775-8085A>G
Ensemble ENST00000295987.13:c.775-8085A>G
Type Transcript Protein
RefSeq NM_003254.2:c.372T>C NP_003245.1:p.Phe124=
Ensemble ENST00000218388.9:c.372T>C ENST00000218388.9:p.Phe124=
ENST00000377017.5:c.180T>C ENST00000377017.5:p.Phe60=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.454
ToMMo:0.449
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.485

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 313440 OMIM
HGNC 11494 HGNC
Ensembl ENSG00000008056 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv66569359 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 305370 OMIM
HGNC 11820 HGNC
Ensembl ENSG00000102265 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv66569359 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-29 criteria provided, single submitter Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 aortic aneurysm No associations with AAA were identified for other SNPs assessed in this study i... BeFree 23813847 Detail
0.129 aortic aneurysm No associations with AAA were identified for other SNPs assessed in this study i... BeFree 23813847 Detail
<0.001 aortic aneurysm No associations with AAA were identified for other SNPs assessed in this study i... BeFree 23813847 Detail
<0.001 aortic aneurysm No associations with AAA were identified for other SNPs assessed in this study i... BeFree 23813847 Detail
0.001 aortic aneurysm No associations with AAA were identified for other SNPs assessed in this study i... BeFree 23813847 Detail
<0.001 aortic aneurysm No associations with AAA were identified for other SNPs assessed in this study i... BeFree 23813847 Detail
0.001 aortic aneurysm No associations with AAA were identified for other SNPs assessed in this study i... BeFree 23813847 Detail
<0.001 Liver diseases We used PCR to analyze 188 patients with HCV-related liver disease (95 with chro... BeFree 23563628 Detail
<0.001 Glaucoma, Primary Open Angle Association of MMP1-1607 1G/2G and TIMP1 372 T/C gene polymorphisms with risk of... BeFree 21709637 Detail
<0.001 Glaucoma, Primary Open Angle Association of MMP1-1607 1G/2G and TIMP1 372 T/C gene polymorphisms with risk of... BeFree 21709637 Detail
0.003 liver cirrhosis We used PCR to analyze 188 patients with HCV-related liver disease (95 with chro... BeFree 23563628 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_006950.3(SYN1):c.775-8085A>G AND Epilepsy, X-linked 1, with variable learning disabilities and be... ClinVar Detail
No associations with AAA were identified for other SNPs assessed in this study including rs1799750 (... DisGeNET Detail
No associations with AAA were identified for other SNPs assessed in this study including rs1799750 (... DisGeNET Detail
No associations with AAA were identified for other SNPs assessed in this study including rs1799750 (... DisGeNET Detail
No associations with AAA were identified for other SNPs assessed in this study including rs1799750 (... DisGeNET Detail
No associations with AAA were identified for other SNPs assessed in this study including rs1799750 (... DisGeNET Detail
No associations with AAA were identified for other SNPs assessed in this study including rs1799750 (... DisGeNET Detail
No associations with AAA were identified for other SNPs assessed in this study including rs1799750 (... DisGeNET Detail
We used PCR to analyze 188 patients with HCV-related liver disease (95 with chronic hepatitis and 93... DisGeNET Detail
Association of MMP1-1607 1G/2G and TIMP1 372 T/C gene polymorphisms with risk of primary open angle ... DisGeNET Detail
Association of MMP1-1607 1G/2G and TIMP1 372 T/C gene polymorphisms with risk of primary open angle ... DisGeNET Detail
We used PCR to analyze 188 patients with HCV-related liver disease (95 with chronic hepatitis and 93... 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
rs4898 dbSNP
Genome
hg19
Position
chrX:47,444,985-47,444,985
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1192
Mean of sample read depth (HGVD)
83.88
Standard deviation of sample read depth (HGVD)
48.13
Number of reference allele (HGVD)
1301
Number of alternative allele (HGVD)
1083
Allele Frequency (HGVD)
0.45427852348993286
Gene Symbol (HGVD)
TIMP1
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))
rs4898
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4487
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5758
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12834
East Asian Chromosome Counts (ExAC)
5418
East Asian Allele Counts (ExAC)
2626
East Asian Heterozygous Counts (ExAC)
1108
East Asian Homozygous Counts (ExAC)
437
East Asian Allele Frequency (ExAC)
0.48468069398301955
Chromosome Counts in All Race (ExAC)
64472
Allele Counts in All Race (ExAC)
34084
Heterozygous Counts in All Race (ExAC)
12899
Homozygous Counts in All Race (ExAC)
5631
Allele Frequency in All Race (ExAC)
0.52866360590644
East Asian Hemizygous Counts (ExAC)
644
Hemizygous Counts in All Race (ExAC)
9923
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