rs2236304
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004995.4(MMP14):c.851-56C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,541,604 control chromosomes in the GnomAD database, including 81,272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.28 ( 6931 hom., cov: 31)
Exomes 𝑓: 0.32 ( 74341 hom. )
Consequence
MMP14
NM_004995.4 intron
NM_004995.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.278
Genes affected
MMP14 (HGNC:7160): (matrix metallopeptidase 14) 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. However, the protein encoded by this gene is a member of the membrane-type MMP (MT-MMP) subfamily; each member of this subfamily contains a potential transmembrane domain suggesting that these proteins are expressed at the cell surface rather than secreted. This protein activates MMP2 protein, and this activity may be involved in tumor invasion. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 14-22843654-C-G is Benign according to our data. Variant chr14-22843654-C-G is described in ClinVar as [Benign]. Clinvar id is 1272389.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP14 | NM_004995.4 | c.851-56C>G | intron_variant | ENST00000311852.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP14 | ENST00000311852.11 | c.851-56C>G | intron_variant | 1 | NM_004995.4 | P1 | |||
MMP14 | ENST00000548162.2 | c.851-56C>G | intron_variant | 5 | |||||
MMP14 | ENST00000680097.1 | c.*166-56C>G | intron_variant, NMD_transcript_variant | ||||||
MMP14 | ENST00000680941.1 | c.*249-56C>G | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.282 AC: 42813AN: 151826Hom.: 6929 Cov.: 31
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GnomAD4 exome AF: 0.322 AC: 447690AN: 1389660Hom.: 74341 Cov.: 28 AF XY: 0.320 AC XY: 219643AN XY: 686788
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GnomAD4 genome ? AF: 0.282 AC: 42819AN: 151944Hom.: 6931 Cov.: 31 AF XY: 0.287 AC XY: 21326AN XY: 74228
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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 | May 14, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at