Variant 11-102842716-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_002422.5(MMP3):c.306C>G(p.Thr102Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0862 in 1,613,822 control chromosomes in the GnomAD database, including 6,341 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.087 ( 603 hom., cov: 30)

Exomes 𝑓: 0.086 ( 5738 hom. )

Consequence

MMP3
NM_002422.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.681

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 -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 11-102842716-G-C is Benign according to our data. Variant chr11-102842716-G-C is described in ClinVar as [Benign]. Clinvar id is 403096.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.681 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMP3	NM_002422.5 linkuse as main transcript	c.306C>G	p.Thr102Thr	synonymous_variant	2/10	ENST00000299855.10	NP_002413.1	P08254

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MMP3	ENST00000299855.10 linkuse as main transcript	c.306C>G	p.Thr102Thr	synonymous_variant	2/10	1	NM_002422.5	ENSP00000299855.5	P08254
MMP3	ENST00000524478.1 linkuse as main transcript	n.*148C>G		non_coding_transcript_exon_variant	2/4	4		ENSP00000435255.1	E9PKX2
MMP3	ENST00000524478.1 linkuse as main transcript	n.*148C>G		3_prime_UTR_variant	2/4	4		ENSP00000435255.1	E9PKX2

Frequencies

GnomAD3 genomes

AF:

0.0874

AC:

13286

AN:

152036

Hom.:

602

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0999

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.0707

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.00308

Gnomad SAS

AF:

0.0661

Gnomad FIN

AF:

0.0592

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.0924

Gnomad OTH

AF:

0.0855

GnomAD3 exomes

AF:

0.0760

AC:

19075

AN:

251098

Hom.:

844

AF XY:

0.0778

AC XY:

10563

AN XY:

135708

show subpopulations

Gnomad AFR exome

AF:

0.0992

Gnomad AMR exome

AF:

0.0474

Gnomad ASJ exome

AF:

0.137

Gnomad EAS exome

AF:

0.00256

Gnomad SAS exome

AF:

0.0690

Gnomad FIN exome

AF:

0.0644

Gnomad NFE exome

AF:

0.0913

Gnomad OTH exome

AF:

0.0869

GnomAD4 exome

AF:

0.0861

AC:

125798

AN:

1461668

Hom.:

5738

Cov.:

AF XY:

0.0862

AC XY:

62699

AN XY:

727110

show subpopulations

Gnomad4 AFR exome

AF:

0.100

Gnomad4 AMR exome

AF:

0.0500

Gnomad4 ASJ exome

AF:

0.133

Gnomad4 EAS exome

AF:

0.00116

Gnomad4 SAS exome

AF:

0.0700

Gnomad4 FIN exome

AF:

0.0666

Gnomad4 NFE exome

AF:

0.0909

Gnomad4 OTH exome

AF:

0.0875

GnomAD4 genome

AF:

0.0874

AC:

13297

AN:

152154

Hom.:

603

Cov.:

AF XY:

0.0859

AC XY:

6385

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.100

Gnomad4 AMR

AF:

0.0706

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.00309

Gnomad4 SAS

AF:

0.0666

Gnomad4 FIN

AF:

0.0592

Gnomad4 NFE

AF:

0.0923

Gnomad4 OTH

AF:

0.0851

Alfa

AF:

0.0521

Hom.:

Bravo

AF:

0.0880

EpiCase

AF:

0.0946

EpiControl

AF:

0.0967

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.30

DANN

Benign

0.30

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