rs1711423
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004771.4(MMP20):c.812-1013A>C 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 152,004 control chromosomes in the GnomAD database, including 13,427 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.41 ( 13425 hom., cov: 31)
Exomes 𝑓: 0.44 ( 2 hom. )
Consequence
MMP20
NM_004771.4 intron
NM_004771.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.537
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
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 | UniProt |
---|---|---|---|---|---|---|---|
MMP20 | NM_004771.4 | c.812-1013A>C | intron_variant | ENST00000260228.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP20 | ENST00000260228.3 | c.812-1013A>C | intron_variant | 1 | NM_004771.4 | P1 | |||
MMP20-AS1 | ENST00000542119.1 | n.86+237T>G | intron_variant, non_coding_transcript_variant | 3 | |||||
MMP20-AS1 | ENST00000544115.1 | n.331-21T>G | intron_variant, non_coding_transcript_variant | 3 | |||||
MMP20 | ENST00000544938.1 | n.155+7A>C | splice_region_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.415 AC: 62955AN: 151870Hom.: 13411 Cov.: 31
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GnomAD4 exome AF: 0.438 AC: 7AN: 16Hom.: 2 Cov.: 0 AF XY: 0.250 AC XY: 2AN XY: 8
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GnomAD4 genome ? AF: 0.414 AC: 62996AN: 151988Hom.: 13425 Cov.: 31 AF XY: 0.412 AC XY: 30610AN XY: 74316
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ClinVar
Not reported inComputational 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