Variant 11-102578919-T-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_004771.4(MMP20):c.1351+120A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 748,500 control chromosomes in the GnomAD database, including 130,255 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.63 ( 30502 hom., cov: 32)

Exomes 𝑓: 0.57 ( 99753 hom. )

Consequence

MMP20
NM_004771.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.418

Variant links:

Genes affected

MMP20 (HGNC:7167): (matrix metallopeptidase 20) 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 protein encoded by this gene degrades amelogenin, the major protein component of dental enamel matrix, and thus thought to play a role in tooth enamel formation. A mutation in this gene, which alters the normal splice pattern and results in premature termination of the encoded protein, has been associated with amelogenesis imperfecta. This gene is part of a cluster of MMP genes located on chromosome 11q22.3. [provided by RefSeq, Aug 2011]

MMP20 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=-0.87).

BP6

Variant 11-102578919-T-A is Benign according to our data. Variant chr11-102578919-T-A is described in ClinVar as [Benign]. Clinvar id is 1241072.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMP20	NM_004771.4 link	c.1351+120A>T		intron_variant		ENST00000260228.3	NP_004762.2	O60882

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MMP20	ENST00000260228.3 link	c.1351+120A>T		intron_variant		1	NM_004771.4	ENSP00000260228.2		O60882
MMP20	ENST00000542305.1 link	n.249+120A>T		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.626

AC:

95186

AN:

151976

Hom.:

30459

Cov.:

show subpopulations

Gnomad AFR

AF:

0.757

Gnomad AMI

AF:

0.424

Gnomad AMR

AF:

0.601

Gnomad ASJ

AF:

0.526

Gnomad EAS

AF:

0.756

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.559

Gnomad OTH

AF:

0.596

GnomAD4 exome

AF:

0.574

AC:

342132

AN:

596406

Hom.:

99753

AF XY:

0.566

AC XY:

182726

AN XY:

322978

show subpopulations

Gnomad4 AFR exome

AF:

0.756

Gnomad4 AMR exome

AF:

0.583

Gnomad4 ASJ exome

AF:

0.526

Gnomad4 EAS exome

AF:

0.786

Gnomad4 SAS exome

AF:

0.484

Gnomad4 FIN exome

AF:

0.624

Gnomad4 NFE exome

AF:

0.556

Gnomad4 OTH exome

AF:

0.585

GnomAD4 genome

AF:

0.626

AC:

95280

AN:

152094

Hom.:

30502

Cov.:

AF XY:

0.629

AC XY:

46739

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.757

Gnomad4 AMR

AF:

0.601

Gnomad4 ASJ

AF:

0.526

Gnomad4 EAS

AF:

0.757

Gnomad4 SAS

AF:

0.495

Gnomad4 FIN

AF:

0.640

Gnomad4 NFE

AF:

0.559

Gnomad4 OTH

AF:

0.598

Alfa

AF:

0.459

Hom.:

1205

Bravo

AF:

0.632

Asia WGS

AF:

0.635

AC:

2207

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	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.8

DANN

Benign

0.53

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