chr8-88327105-G-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005941.5(MMP16):c.102C>G(p.Val34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000387 in 1,613,996 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0021 ( 2 hom., cov: 31)
Exomes 𝑓: 0.00021 ( 1 hom. )
Consequence
MMP16
NM_005941.5 synonymous
NM_005941.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.88
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 8-88327105-G-C is Benign according to our data. Variant chr8-88327105-G-C is described in ClinVar as [Benign]. Clinvar id is 776362.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.88 with no splicing effect.
BS2
?
High AC in GnomAd at 323 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP16 | NM_005941.5 | c.102C>G | p.Val34= | synonymous_variant | 1/10 | ENST00000286614.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP16 | ENST00000286614.11 | c.102C>G | p.Val34= | synonymous_variant | 1/10 | 1 | NM_005941.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00212 AC: 323AN: 152048Hom.: 2 Cov.: 31
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GnomAD3 exomes AF: 0.000461 AC: 116AN: 251484Hom.: 1 AF XY: 0.000324 AC XY: 44AN XY: 135920
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GnomAD4 exome AF: 0.000207 AC: 303AN: 1461830Hom.: 1 Cov.: 31 AF XY: 0.000184 AC XY: 134AN XY: 727220
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GnomAD4 genome ? AF: 0.00212 AC: 322AN: 152166Hom.: 2 Cov.: 31 AF XY: 0.00190 AC XY: 141AN XY: 74394
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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 | Invitae | May 31, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at