Variant 11-102838730-CAG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002422.5(MMP3):c.1070-22_1070-21del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0192 in 1,603,720 control chromosomes in the GnomAD database, including 2,215 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.055 ( 618 hom., cov: 32)

Exomes 𝑓: 0.016 ( 1597 hom. )

Consequence

MMP3
NM_002422.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.529

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-102838730-CAG-C is Benign according to our data. Variant chr11-102838730-CAG-C is described in ClinVar as [Benign]. Clinvar id is 1246283.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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.1070-22_1070-21del		intron_variant		ENST00000299855.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMP3	ENST00000299855.10 linkuse as main transcript	c.1070-22_1070-21del		intron_variant		1	NM_002422.5	P1
MMP3	ENST00000434103.1 linkuse as main transcript			upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0545

AC:

8280

AN:

152052

Hom.:

617

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0182

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.187

Gnomad SAS

AF:

0.0866

Gnomad FIN

AF:

0.0000943

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00115

Gnomad OTH

AF:

0.0402

GnomAD3 exomes

AF:

0.0370

AC:

9094

AN:

245506

Hom.:

678

AF XY:

0.0359

AC XY:

4776

AN XY:

132944

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.00742

Gnomad ASJ exome

AF:

0.00201

Gnomad EAS exome

AF:

0.200

Gnomad SAS exome

AF:

0.0838

Gnomad FIN exome

AF:

0.0000468

Gnomad NFE exome

AF:

0.00126

Gnomad OTH exome

AF:

0.0206

GnomAD4 exome

AF:

0.0155

AC:

22530

AN:

1451550

Hom.:

1597

AF XY:

0.0167

AC XY:

12088

AN XY:

722600

show subpopulations

Gnomad4 AFR exome

AF:

0.164

Gnomad4 AMR exome

AF:

0.00865

Gnomad4 ASJ exome

AF:

0.00277

Gnomad4 EAS exome

AF:

0.180

Gnomad4 SAS exome

AF:

0.0800

Gnomad4 FIN exome

AF:

0.0000376

Gnomad4 NFE exome

AF:

0.000836

Gnomad4 OTH exome

AF:

0.0291

GnomAD4 genome

AF:

0.0545

AC:

8297

AN:

152170

Hom.:

618

Cov.:

AF XY:

0.0547

AC XY:

4071

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.0182

Gnomad4 ASJ

AF:

0.00403

Gnomad4 EAS

AF:

0.187

Gnomad4 SAS

AF:

0.0856

Gnomad4 FIN

AF:

0.0000943

Gnomad4 NFE

AF:

0.00115

Gnomad4 OTH

AF:

0.0445

Alfa

AF:

0.0229

Hom.:

Bravo

AF:

0.0596

Asia WGS

AF:

0.183

AC:

635

AN:

3478

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

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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