Variant chr11-102608807-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_004771.4(MMP20):c.811+130T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 990,358 control chromosomes in the GnomAD database, including 27,776 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.24 ( 4687 hom., cov: 34)

Exomes 𝑓: 0.23 ( 23089 hom. )

Consequence

MMP20
NM_004771.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.124

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:

MMP20-AS1 (HGNC:56362): (MMP20 antisense RNA 1)

MMP20-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 11-102608807-A-G is Benign according to our data. Variant chr11-102608807-A-G is described in ClinVar as [Benign]. Clinvar id is 1222934.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMP20	NM_004771.4 linkuse as main transcript	c.811+130T>C		intron_variant		ENST00000260228.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMP20	ENST00000260228.3 linkuse as main transcript	c.811+130T>C		intron_variant		1	NM_004771.4	P1
MMP20-AS1	ENST00000542119.1 linkuse as main transcript	n.86+1355A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36940

AN:

152132

Hom.:

4675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.128

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.313

Gnomad EAS

AF:

0.0217

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.239

GnomAD4 exome

AF:

0.230

AC:

192790

AN:

838108

Hom.:

23089

AF XY:

0.230

AC XY:

101093

AN XY:

440180

show subpopulations

Gnomad4 AFR exome

AF:

0.283

Gnomad4 AMR exome

AF:

0.253

Gnomad4 ASJ exome

AF:

0.308

Gnomad4 EAS exome

AF:

0.0325

Gnomad4 SAS exome

AF:

0.222

Gnomad4 FIN exome

AF:

0.219

Gnomad4 NFE exome

AF:

0.238

Gnomad4 OTH exome

AF:

0.233

GnomAD4 genome

AF:

0.243

AC:

36980

AN:

152250

Hom.:

4687

Cov.:

AF XY:

0.242

AC XY:

17980

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.282

Gnomad4 AMR

AF:

0.249

Gnomad4 ASJ

AF:

0.313

Gnomad4 EAS

AF:

0.0220

Gnomad4 SAS

AF:

0.203

Gnomad4 FIN

AF:

0.216

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.237

Alfa

AF:

0.247

Hom.:

585

Bravo

AF:

0.243

Asia WGS

AF:

0.112

AC:

390

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

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.2

DANN

Benign

0.77

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