11-102578800-A-AAAAC
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_004771.4(MMP20):c.1351+235_1351+238dupGTTT 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 ( 8669 hom., cov: 0)
Consequence
MMP20
NM_004771.4 intron
NM_004771.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.88
Publications
0 publications found
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 Gene-Disease associations (from GenCC):
- amelogenesis imperfecta hypomaturation type 2A2Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- amelogenesis imperfecta type 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 11-102578800-A-AAAAC is Benign according to our data. Variant chr11-102578800-A-AAAAC is described in ClinVar as [Benign]. Clinvar id is 1280440.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.332 AC: 50236AN: 151176Hom.: 8673 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
50236
AN:
151176
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.332 AC: 50244AN: 151296Hom.: 8669 Cov.: 0 AF XY: 0.339 AC XY: 25057AN XY: 73936 show subpopulations
GnomAD4 genome
AF:
AC:
50244
AN:
151296
Hom.:
Cov.:
0
AF XY:
AC XY:
25057
AN XY:
73936
show subpopulations
African (AFR)
AF:
AC:
13638
AN:
41134
American (AMR)
AF:
AC:
6062
AN:
15226
Ashkenazi Jewish (ASJ)
AF:
AC:
813
AN:
3462
East Asian (EAS)
AF:
AC:
2769
AN:
5142
South Asian (SAS)
AF:
AC:
1553
AN:
4810
European-Finnish (FIN)
AF:
AC:
4272
AN:
10472
Middle Eastern (MID)
AF:
AC:
87
AN:
292
European-Non Finnish (NFE)
AF:
AC:
20190
AN:
67744
Other (OTH)
AF:
AC:
688
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
1572
3143
4715
6286
7858
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 19, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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