11-102578736-AAAAAAACAAAAAAC-A

Position:

• chr11-102578736-AAAAAAACAAAAAAC-A

Variant summary

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

The NM_004771.4(MMP20):​c.1351+289_1351+302del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.33 (9455 hom., cov: 0)
• Consequence: MMP20 NM_004771.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.591

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-102578736-AAAAAAACAAAAAAC-A is Benign according to our data. Variant chr11-102578736-AAAAAAACAAAAAAC-A is described in ClinVar as [Benign]. Clinvar id is 1266612.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMP20	NM_004771.4	c.1351+289_1351+302del		intron_variant		ENST00000260228.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMP20	ENST00000260228.3	c.1351+289_1351+302del		intron_variant		1	NM_004771.4	P1
MMP20	ENST00000542305.1	n.249+289_249+302del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49095 AN: 150488 Hom.: 9454 Cov.: 0

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.326 AC: 49105 AN: 150606 Hom.: 9455 Cov.: 0 AF XY: 0.323 AC XY: 23756 AN XY: 73482

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.367

Alfa AF: 0.390 Hom.: 792

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

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs147058509; hg19: chr11-102449467;