11-102608692-C-CA

Position:

• chr11-102608692-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_004771.4(MMP20):​c.811+244_811+245insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,728 control chromosomes in the GnomAD database, including 13,313 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.41 (13313 hom., cov: 32)
• Consequence: MMP20 NM_004771.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.916

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-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-102608692-C-CA is Benign according to our data. Variant chr11-102608692-C-CA is described in ClinVar as [Benign]. Clinvar id is 1275519.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MMP20	NM_004771.4	c.811+244_811+245insT		intron_variant		ENST00000260228.3	NP_004762.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MMP20	ENST00000260228.3	c.811+244_811+245insT		intron_variant		1	NM_004771.4	ENSP00000260228.2
MMP20-AS1	ENST00000542119.1	n.86+1240_86+1241insA		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62770 AN: 151610 Hom.: 13299 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.447

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.414 AC: 62811 AN: 151728 Hom.: 13313 Cov.: 32 AF XY: 0.411 AC XY: 30471 AN XY: 74120

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.454

Alfa AF: 0.380 Hom.: 329

Asia WGS AF: 0.546 AC: 1902 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs376710103; hg19: chr11-102479423;