Genetic Variant MMP9:c.-154_-147delCACACACA (chr20-46008772-CCACACACA-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004994.3(MMP9):c.-154_-147delCACACACA variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0194 in 993,286 control chromosomes in the GnomAD database, including 104 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.021 ( 44 hom., cov: 0)

Exomes 𝑓: 0.019 ( 60 hom. )

Consequence

MMP9
NM_004994.3 upstream_gene

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.281

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MMP9	NM_004994.3 link	c.-154_-147delCACACACA		upstream_gene_variant		ENST00000372330.3	NP_004985.2	P14780

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMP9	ENST00000372330.3 link	c.-154_-147delCACACACA		upstream_gene_variant		1	NM_004994.3	ENSP00000361405.3		P14780

Frequencies

GnomAD3 genomes

AF:

0.0208

AC:

2949

AN:

141488

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0218

Gnomad AMI

AF:

0.00112

Gnomad AMR

AF:

0.0193

Gnomad ASJ

AF:

0.0242

Gnomad EAS

AF:

0.0190

Gnomad SAS

AF:

0.0928

Gnomad FIN

AF:

0.0327

Gnomad MID

AF:

0.0161

Gnomad NFE

AF:

0.0145

Gnomad OTH

AF:

0.0236

GnomAD4 exome

AF:

0.0191

AC:

16274

AN:

851696

Hom.:

AF XY:

0.0211

AC XY:

9141

AN XY:

433774

show subpopulations

Gnomad4 AFR exome

AF:

0.0362

Gnomad4 AMR exome

AF:

0.0159

Gnomad4 ASJ exome

AF:

0.0252

Gnomad4 EAS exome

AF:

0.0385

Gnomad4 SAS exome

AF:

0.0718

Gnomad4 FIN exome

AF:

0.0298

Gnomad4 NFE exome

AF:

0.0116

Gnomad4 OTH exome

AF:

0.0217

GnomAD4 genome

AF:

0.0208

AC:

2948

AN:

141590

Hom.:

Cov.:

AF XY:

0.0228

AC XY:

1559

AN XY:

68260

show subpopulations

Gnomad4 AFR

AF:

0.0219

Gnomad4 AMR

AF:

0.0192

Gnomad4 ASJ

AF:

0.0242

Gnomad4 EAS

AF:

0.0184

Gnomad4 SAS

AF:

0.0923

Gnomad4 FIN

AF:

0.0327

Gnomad4 NFE

AF:

0.0145

Gnomad4 OTH

AF:

0.0239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

20-46008772-CCACACACACACACACACACACACACACACACACA-CCACACACACACACACACACACACACA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over