Genetic Variant MMP16:c.*2392G>A (chr8-88039069-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.26

Variant links:

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]

MMP16 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 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_multiple_submitters_no_conflicts, 2 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 rank	MANE	Protein	UniProt
MMP16	NM_005941.5 link	c.*2392G>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000286614.11	NP_005932.2	P51512-1
MMP16	XM_024447154.2 link	c.*2392G>A		3_prime_UTR_variant	Exon 7 of 7		XP_024302922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MMP16	ENST00000286614 link	c.*2392G>A		3_prime_UTR_variant	Exon 10 of 10	1	NM_005941.5	ENSP00000286614.6		P51512-1

Frequencies

GnomAD3 genomes

AF:

0.569

AC:

86315

AN:

151686

Hom.:

24712

Cov.:

show subpopulations

Gnomad AFR

AF:

0.535

Gnomad AMI

AF:

0.672

Gnomad AMR

AF:

0.657

Gnomad ASJ

AF:

0.584

Gnomad EAS

AF:

0.683

Gnomad SAS

AF:

0.550

Gnomad FIN

AF:

0.514

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.569

GnomAD4 exome

AF:

0.533

AC:

229

AN:

430

Hom.:

Cov.:

AF XY:

0.504

AC XY:

131

AN XY:

260

show subpopulations

Gnomad4 FIN exome

AF:

0.531

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.750

GnomAD4 genome

AF:

0.569

AC:

86396

AN:

151806

Hom.:

24743

Cov.:

AF XY:

0.568

AC XY:

42160

AN XY:

74186

show subpopulations

Gnomad4 AFR

AF:

0.536

Gnomad4 AMR

AF:

0.657

Gnomad4 ASJ

AF:

0.584

Gnomad4 EAS

AF:

0.683

Gnomad4 SAS

AF:

0.547

Gnomad4 FIN

AF:

0.514

Gnomad4 NFE

AF:

0.569

Gnomad4 OTH

AF:

0.570

Alfa

AF:

0.573

Hom.:

35508

Bravo

AF:

0.578

Asia WGS

AF:

0.629

AC:

2180

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Oct 29, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 32196811) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over