Variant chr11-102837183-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002422.5(MMP3):c.1333+115T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 706,526 control chromosomes in the GnomAD database, including 105,171 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.55 ( 23049 hom., cov: 32)

Exomes 𝑓: 0.54 ( 82122 hom. )

Consequence

MMP3
NM_002422.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.713

Variant links:

Genes affected

MMP3 (HGNC:7173): (matrix metallopeptidase 3) 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. This gene encodes an enzyme which degrades fibronectin, laminin, collagens III, IV, IX, and X, and cartilage proteoglycans. The enzyme is thought to be involved in wound repair, progression of atherosclerosis, and tumor initiation. The gene is part of a cluster of MMP genes which localize to chromosome 11q22.3. [provided by RefSeq, Jul 2008]

MMP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 11-102837183-A-G is Benign according to our data. Variant chr11-102837183-A-G is described in ClinVar as [Benign]. Clinvar id is 1286978.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMP3	NM_002422.5 linkuse as main transcript	c.1333+115T>C		intron_variant		ENST00000299855.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMP3	ENST00000299855.10 linkuse as main transcript	c.1333+115T>C		intron_variant		1	NM_002422.5	P1
MMP3	ENST00000434103.1 linkuse as main transcript	c.264+115T>C		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.546

AC:

82940

AN:

151890

Hom.:

23016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.552

Gnomad AMI

AF:

0.581

Gnomad AMR

AF:

0.628

Gnomad ASJ

AF:

0.614

Gnomad EAS

AF:

0.678

Gnomad SAS

AF:

0.697

Gnomad FIN

AF:

0.607

Gnomad MID

AF:

0.566

Gnomad NFE

AF:

0.490

Gnomad OTH

AF:

0.538

GnomAD4 exome

AF:

0.537

AC:

297934

AN:

554518

Hom.:

82122

AF XY:

0.543

AC XY:

158237

AN XY:

291320

show subpopulations

Gnomad4 AFR exome

AF:

0.554

Gnomad4 AMR exome

AF:

0.670

Gnomad4 ASJ exome

AF:

0.607

Gnomad4 EAS exome

AF:

0.684

Gnomad4 SAS exome

AF:

0.678

Gnomad4 FIN exome

AF:

0.589

Gnomad4 NFE exome

AF:

0.486

Gnomad4 OTH exome

AF:

0.542

GnomAD4 genome

AF:

0.546

AC:

83024

AN:

152008

Hom.:

23049

Cov.:

AF XY:

0.555

AC XY:

41269

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.552

Gnomad4 AMR

AF:

0.628

Gnomad4 ASJ

AF:

0.614

Gnomad4 EAS

AF:

0.677

Gnomad4 SAS

AF:

0.697

Gnomad4 FIN

AF:

0.607

Gnomad4 NFE

AF:

0.490

Gnomad4 OTH

AF:

0.539

Alfa

AF:

0.510

Hom.:

4497

Bravo

AF:

0.547

Asia WGS

AF:

0.663

AC:

2304

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.27

DANN

Benign

0.51

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