11-102608692-C-CA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_004771.4(MMP20):c.811+244_811+245insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,728 control chromosomes in the GnomAD database, including 13,313 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.41 ( 13313 hom., cov: 32)
Consequence
MMP20
NM_004771.4 intron
NM_004771.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.916
Genes affected
MMP20 (HGNC:7167): (matrix metallopeptidase 20) 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 protein encoded by this gene degrades amelogenin, the major protein component of dental enamel matrix, and thus thought to play a role in tooth enamel formation. A mutation in this gene, which alters the normal splice pattern and results in premature termination of the encoded protein, has been associated with amelogenesis imperfecta. This gene is part of a cluster of MMP genes located on chromosome 11q22.3. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 11-102608692-C-CA is Benign according to our data. Variant chr11-102608692-C-CA is described in ClinVar as [Benign]. Clinvar id is 1275519.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMP20 | NM_004771.4 | c.811+244_811+245insT | intron_variant | ENST00000260228.3 | NP_004762.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MMP20 | ENST00000260228.3 | c.811+244_811+245insT | intron_variant | 1 | NM_004771.4 | ENSP00000260228.2 | ||||
MMP20-AS1 | ENST00000542119.1 | n.86+1240_86+1241insA | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.414 AC: 62770AN: 151610Hom.: 13299 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.414 AC: 62811AN: 151728Hom.: 13313 Cov.: 32 AF XY: 0.411 AC XY: 30471AN XY: 74120
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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 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at