GeneBe

rs2234681

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_004994.3(MMP9):​c.-154_-121delCACACACACACACACACACACACACACACACACA variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000175 in 854,882 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

MMP9
NM_004994.3 upstream_gene

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65

Publications

0 publications found
Variant links:
Genes affected
MMP9 (HGNC:7176): (matrix metallopeptidase 9) Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when cleaved by extracellular proteinases. The enzyme encoded by this gene degrades type IV and V collagens. Studies in rhesus monkeys suggest that the enzyme is involved in IL-8-induced mobilization of hematopoietic progenitor cells from bone marrow, and murine studies suggest a role in tumor-associated tissue remodeling. [provided by RefSeq, Jul 2008]
MMP9 Gene-Disease associations (from GenCC):
  • metaphyseal anadysplasia
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • metaphyseal anadysplasia 2
    Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2
High AC in GnomAdExome4 at 15 Unknown,AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MMP9NM_004994.3 linkc.-154_-121delCACACACACACACACACACACACACACACACACA upstream_gene_variant ENST00000372330.3 NP_004985.2 P14780

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MMP9ENST00000372330.3 linkc.-154_-121delCACACACACACACACACACACACACACACACACA upstream_gene_variant 1 NM_004994.3 ENSP00000361405.3 P14780

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.0000175
AC:
15
AN:
854882
Hom.:
0
AF XY:
0.00000919
AC XY:
4
AN XY:
435426
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
18950
American (AMR)
AF:
0.00
AC:
0
AN:
31658
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19556
East Asian (EAS)
AF:
0.00
AC:
0
AN:
28172
South Asian (SAS)
AF:
0.00
AC:
0
AN:
63516
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
31422
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2964
European-Non Finnish (NFE)
AF:
0.0000242
AC:
15
AN:
620080
Other (OTH)
AF:
0.00
AC:
0
AN:
38564
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2234681; hg19: chr20-44637411; API