11-102608687-T-C

Variant summary

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

The NM_004771.4(MMP20):​c.811+250A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 151,882 control chromosomes in the GnomAD database, including 42,533 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.75 ( 42533 hom., cov: 33)

Consequence

MMP20
NM_004771.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.69
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]

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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=-0.98).
BP6
Variant 11-102608687-T-C is Benign according to our data. Variant chr11-102608687-T-C is described in ClinVar as [Benign]. Clinvar id is 1228002.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MMP20NM_004771.4 linkuse as main transcriptc.811+250A>G intron_variant ENST00000260228.3 NP_004762.2 O60882

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MMP20ENST00000260228.3 linkuse as main transcriptc.811+250A>G intron_variant 1 NM_004771.4 ENSP00000260228.2 O60882
MMP20-AS1ENST00000542119.1 linkuse as main transcriptn.86+1235T>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.746
AC:
113284
AN:
151764
Hom.:
42506
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.683
Gnomad AMI
AF:
0.871
Gnomad AMR
AF:
0.744
Gnomad ASJ
AF:
0.687
Gnomad EAS
AF:
0.978
Gnomad SAS
AF:
0.797
Gnomad FIN
AF:
0.784
Gnomad MID
AF:
0.667
Gnomad NFE
AF:
0.760
Gnomad OTH
AF:
0.748
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.746
AC:
113357
AN:
151882
Hom.:
42533
Cov.:
33
AF XY:
0.748
AC XY:
55497
AN XY:
74214
show subpopulations
Gnomad4 AFR
AF:
0.683
Gnomad4 AMR
AF:
0.744
Gnomad4 ASJ
AF:
0.687
Gnomad4 EAS
AF:
0.978
Gnomad4 SAS
AF:
0.796
Gnomad4 FIN
AF:
0.784
Gnomad4 NFE
AF:
0.760
Gnomad4 OTH
AF:
0.751
Alfa
AF:
0.744
Hom.:
5325
Bravo
AF:
0.745
Asia WGS
AF:
0.885
AC:
3076
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 submitterclinical testingGeneDxNov 12, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
1.1
DANN
Benign
0.49

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.

Other links and lift over

dbSNP: rs2509019; hg19: chr11-102479418; API