chr20:46013767:G>C Detail (hg38) (MMP9, SLC12A5-AS1)

Information

Genome

Assembly Position
hg19 chr20:44,642,406-44,642,406 View the variant detail on this assembly version.
hg38 chr20:46,013,767-46,013,767

HGVS

Type Transcript Protein
RefSeq NM_004994.2:c.1721G>C NP_004985.2:p.Arg574Pro
Ensemble ENST00000372330.3:c.1721G>C ENST00000372330.3:p.Arg574Pro
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.689
ToMMo:0.698
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.772

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 120361 OMIM
HGNC 7176 HGNC
Ensembl ENSG00000100985 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv63869476 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2015-11-09 criteria provided, single submitter not specified germline Detail
Benign 2021-09-05 criteria provided, multiple submitters, no conflicts Metaphyseal anadysplasia 2 germline unknown Detail
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.011 coronary artery disease We explored the association of MMP2 (C-735T, rs2285053), MMP7 (A-181G, rs1156881... BeFree 22664146 Detail
0.030 coronary artery disease These findings suggest that MMP-9 R279Q, P574R and R668Q may have combined effec... BeFree 19283512 Detail
0.002 Squamous cell carcinoma of esophagus Our study shows for the first time that MMP-9 gene P574R polymorphism may contri... BeFree 18680431 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004994.3(MMP9):c.1721G>C (p.Arg574Pro) AND not specified ClinVar Detail
NM_004994.3(MMP9):c.1721G>C (p.Arg574Pro) AND Metaphyseal anadysplasia 2 ClinVar Detail
NM_004994.3(MMP9):c.1721G>C (p.Arg574Pro) AND not provided ClinVar Detail
We explored the association of MMP2 (C-735T, rs2285053), MMP7 (A-181G, rs11568818) and MMP9 (R279Q, ... DisGeNET Detail
These findings suggest that MMP-9 R279Q, P574R and R668Q may have combined effect in the occurrence ... DisGeNET Detail
Our study shows for the first time that MMP-9 gene P574R polymorphism may contribute to a genetic ri... 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
rs2250889 dbSNP
Genome
hg38
Position
chr20:46,013,767-46,013,767
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1186
Mean of sample read depth (HGVD)
56.02
Standard deviation of sample read depth (HGVD)
23.24
Number of reference allele (HGVD)
737
Number of alternative allele (HGVD)
1633
Allele Frequency (HGVD)
0.689029535864979
Gene Symbol (HGVD)
MMP9
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))
rs2250889
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6979
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11696
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8616
East Asian Allele Counts (ExAC)
6655
East Asian Heterozygous Counts (ExAC)
1523
East Asian Homozygous Counts (ExAC)
2566
East Asian Allele Frequency (ExAC)
0.7724001857010213
Chromosome Counts in All Race (ExAC)
120918
Allele Counts in All Race (ExAC)
106884
Heterozygous Counts in All Race (ExAC)
10889
Homozygous Counts in All Race (ExAC)
47995
Allele Frequency in All Race (ExAC)
0.8839378752543046
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