Variant chr11-102836574-G-A 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.1334-348C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 485,038 control chromosomes in the GnomAD database, including 4,440 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 1229 hom., cov: 32)

Exomes 𝑓: 0.13 ( 3211 hom. )

Consequence

MMP3
NM_002422.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.607

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:

WTAPP1 (HGNC:44115): (WTAP pseudogene 1)

WTAPP1 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=-0.91).

BP6

Variant 11-102836574-G-A is Benign according to our data. Variant chr11-102836574-G-A is described in ClinVar as [Benign]. Clinvar id is 1263820.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 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.1334-348C>T		intron_variant		ENST00000299855.10
WTAPP1	NR_038390.1 linkuse as main transcript	n.2450G>A		non_coding_transcript_exon_variant	8/8

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris
MMP3	ENST00000299855.10 linkuse as main transcript	c.1334-348C>T	intron_variant		1	NM_002422.5	P1
MMP3	ENST00000434103.1 linkuse as main transcript	c.265-46C>T	intron_variant		3
WTAPP1	ENST00000525739.6 linkuse as main transcript	n.2450G>A	non_coding_transcript_exon_variant	8/8	2

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15855

AN:

151982

Hom.:

1229

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0248

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.0839

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.0719

Gnomad SAS

AF:

0.0781

Gnomad FIN

AF:

0.278

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.120

AC:

18070

AN:

150284

Hom.:

1438

AF XY:

0.119

AC XY:

9545

AN XY:

80504

show subpopulations

Gnomad AFR exome

AF:

0.0203

Gnomad AMR exome

AF:

0.0748

Gnomad ASJ exome

AF:

0.131

Gnomad EAS exome

AF:

0.0712

Gnomad SAS exome

AF:

0.0820

Gnomad FIN exome

AF:

0.255

Gnomad NFE exome

AF:

0.135

Gnomad OTH exome

AF:

0.126

GnomAD4 exome

AF:

0.127

AC:

42184

AN:

332938

Hom.:

3211

Cov.:

AF XY:

0.124

AC XY:

23162

AN XY:

187376

show subpopulations

Gnomad4 AFR exome

AF:

0.0235

Gnomad4 AMR exome

AF:

0.0746

Gnomad4 ASJ exome

AF:

0.133

Gnomad4 EAS exome

AF:

0.0838

Gnomad4 SAS exome

AF:

0.0849

Gnomad4 FIN exome

AF:

0.247

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.123

GnomAD4 genome

AF:

0.104

AC:

15855

AN:

152100

Hom.:

1229

Cov.:

AF XY:

0.108

AC XY:

8057

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.0247

Gnomad4 AMR

AF:

0.0838

Gnomad4 ASJ

AF:

0.126

Gnomad4 EAS

AF:

0.0719

Gnomad4 SAS

AF:

0.0786

Gnomad4 FIN

AF:

0.278

Gnomad4 NFE

AF:

0.133

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.122

Hom.:

279

Bravo

AF:

0.0873

Asia WGS

AF:

0.0690

AC:

239

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.70

DANN

Benign

0.72

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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