11-102838730-CAG-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_002422.5(MMP3):c.1070-22_1070-21delCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0192 in 1,603,720 control chromosomes in the GnomAD database, including 2,215 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.055 ( 618 hom., cov: 32)
Exomes 𝑓: 0.016 ( 1597 hom. )
Consequence
MMP3
NM_002422.5 intron
NM_002422.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.529
Genes affected
MMP3 (HGNC:7173): (matrix metallopeptidase 3) 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. This gene encodes an enzyme which degrades fibronectin, laminin, collagens III, IV, IX, and X, and cartilage proteoglycans. The enzyme is thought to be involved in wound repair, progression of atherosclerosis, and tumor initiation. The gene is part of a cluster of MMP genes which localize to chromosome 11q22.3. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 11-102838730-CAG-C is Benign according to our data. Variant chr11-102838730-CAG-C is described in ClinVar as [Benign]. Clinvar id is 1246283.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMP3 | NM_002422.5 | c.1070-22_1070-21delCT | intron_variant | ENST00000299855.10 | NP_002413.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MMP3 | ENST00000299855.10 | c.1070-22_1070-21delCT | intron_variant | 1 | NM_002422.5 | ENSP00000299855.5 | ||||
MMP3 | ENST00000434103.1 | c.-24_-23delCT | upstream_gene_variant | 3 | ENSP00000398346.1 |
Frequencies
GnomAD3 genomes AF: 0.0545 AC: 8280AN: 152052Hom.: 617 Cov.: 32
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GnomAD3 exomes AF: 0.0370 AC: 9094AN: 245506Hom.: 678 AF XY: 0.0359 AC XY: 4776AN XY: 132944
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GnomAD4 exome AF: 0.0155 AC: 22530AN: 1451550Hom.: 1597 AF XY: 0.0167 AC XY: 12088AN XY: 722600
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GnomAD4 genome AF: 0.0545 AC: 8297AN: 152170Hom.: 618 Cov.: 32 AF XY: 0.0547 AC XY: 4071AN XY: 74402
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at