rs13969
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_004994.3(MMP9):āc.1821A>Cā(p.Gly607=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 1,537,284 control chromosomes in the GnomAD database, including 257,695 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.53 ( 21915 hom., cov: 33)
Exomes š: 0.58 ( 235780 hom. )
Consequence
MMP9
NM_004994.3 synonymous
NM_004994.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.24
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
?
Variant 20-46014194-A-C is Benign according to our data. Variant chr20-46014194-A-C is described in ClinVar as [Benign]. Clinvar id is 285363.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-46014194-A-C is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-2.24 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP9 | NM_004994.3 | c.1821A>C | p.Gly607= | synonymous_variant | 11/13 | ENST00000372330.3 | |
SLC12A5-AS1 | NR_147699.1 | n.1263T>G | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP9 | ENST00000372330.3 | c.1821A>C | p.Gly607= | synonymous_variant | 11/13 | 1 | NM_004994.3 | P1 | |
SLC12A5-AS1 | ENST00000535913.2 | n.1263T>G | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.528 AC: 80229AN: 151966Hom.: 21914 Cov.: 33
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GnomAD3 exomes AF: 0.499 AC: 67779AN: 135832Hom.: 17974 AF XY: 0.497 AC XY: 36750AN XY: 73898
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GnomAD4 exome AF: 0.577 AC: 799523AN: 1385202Hom.: 235780 Cov.: 63 AF XY: 0.573 AC XY: 391217AN XY: 683186
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GnomAD4 genome ? AF: 0.528 AC: 80263AN: 152082Hom.: 21915 Cov.: 33 AF XY: 0.521 AC XY: 38745AN XY: 74348
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Metaphyseal anadysplasia 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 28, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at