chr8-88039069-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005941.5(MMP16):c.*2392G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,236 control chromosomes in the GnomAD database, including 24,803 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.57 ( 24743 hom., cov: 32)
Exomes 𝑓: 0.53 ( 60 hom. )
Consequence
MMP16
NM_005941.5 3_prime_UTR
NM_005941.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.26
Genes affected
MMP16 (HGNC:7162): (matrix metallopeptidase 16) 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 encoded protein activates MMP2 by cleavage. This gene was once referred to as MT-MMP2, but was renamed as MT-MMP3 or MMP16. [provided by RefSeq, Oct 2010]
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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=-0.58).
BP6
?
Variant 8-88039069-C-T is Benign according to our data. Variant chr8-88039069-C-T is described in ClinVar as [Benign]. Clinvar id is 1270817.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP16 | NM_005941.5 | c.*2392G>A | 3_prime_UTR_variant | 10/10 | ENST00000286614.11 | ||
MMP16 | XM_024447154.2 | c.*2392G>A | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP16 | ENST00000286614.11 | c.*2392G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_005941.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.569 AC: 86315AN: 151686Hom.: 24712 Cov.: 32
GnomAD3 genomes
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GnomAD4 exome AF: 0.533 AC: 229AN: 430Hom.: 60 Cov.: 0 AF XY: 0.504 AC XY: 131AN XY: 260
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GnomAD4 genome ? AF: 0.569 AC: 86396AN: 151806Hom.: 24743 Cov.: 32 AF XY: 0.568 AC XY: 42160AN XY: 74186
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3470
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 | Oct 29, 2020 | This variant is associated with the following publications: (PMID: 32196811) - |
Computational scores
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Name
Calibrated prediction
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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