rs9509
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004994.3(MMP9):c.*146T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0703 in 709,702 control chromosomes in the GnomAD database, including 4,210 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.11 ( 1727 hom., cov: 31)
Exomes 𝑓: 0.059 ( 2483 hom. )
Consequence
MMP9
NM_004994.3 3_prime_UTR
NM_004994.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0710
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 20-46016514-T-C is Benign according to our data. Variant chr20-46016514-T-C is described in ClinVar as [Benign]. Clinvar id is 338563.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP9 | NM_004994.3 | c.*146T>C | 3_prime_UTR_variant | 13/13 | ENST00000372330.3 | ||
SLC12A5-AS1 | NR_147699.1 | n.669-1726A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP9 | ENST00000372330.3 | c.*146T>C | 3_prime_UTR_variant | 13/13 | 1 | NM_004994.3 | P1 | ||
SLC12A5-AS1 | ENST00000535913.2 | n.669-1726A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.112 AC: 16982AN: 152042Hom.: 1724 Cov.: 31
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GnomAD4 exome AF: 0.0591 AC: 32923AN: 557542Hom.: 2483 Cov.: 6 AF XY: 0.0561 AC XY: 16761AN XY: 299022
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GnomAD4 genome ? AF: 0.112 AC: 17001AN: 152160Hom.: 1727 Cov.: 31 AF XY: 0.113 AC XY: 8398AN XY: 74392
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Metaphyseal anadysplasia 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 31, 2019 | - - |
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