11-102578792-C-CAA

Position:

• chr11-102578792-C-CAA

Variant summary

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

The NM_004771.4(MMP20):​c.1351+246_1351+247insTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 136,508 control chromosomes in the GnomAD database, including 4,845 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.27 (4845 hom., cov: 25)
• Consequence: MMP20 NM_004771.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.75

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 11-102578792-C-CAA is Benign according to our data. Variant chr11-102578792-C-CAA is described in ClinVar as [Benign]. Clinvar id is 1289239.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMP20	NM_004771.4	c.1351+246_1351+247insTT		intron_variant		ENST00000260228.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMP20	ENST00000260228.3	c.1351+246_1351+247insTT		intron_variant		1	NM_004771.4	P1
MMP20	ENST00000542305.1	n.249+246_249+247insTT		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.267 AC: 36433 AN: 136380 Hom.: 4838 Cov.: 25

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.267 AC: 36484 AN: 136508 Hom.: 4845 Cov.: 25 AF XY: 0.267 AC XY: 17657 AN XY: 66172

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.198

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.241

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

- -

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: rs141523340; hg19: chr11-102449523;