chr11-102590046-G-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004771.4(MMP20):c.1247+3393C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 151,892 control chromosomes in the GnomAD database, including 20,232 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.51 ( 20232 hom., cov: 31)
Consequence
MMP20
NM_004771.4 intron
NM_004771.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0980
Publications
8 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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.509 AC: 77191AN: 151774Hom.: 20221 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
77191
AN:
151774
Hom.:
Cov.:
31
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 AF: 0.508 AC: 77218AN: 151892Hom.: 20232 Cov.: 31 AF XY: 0.508 AC XY: 37676AN XY: 74238 show subpopulations
GnomAD4 genome
AF:
AC:
77218
AN:
151892
Hom.:
Cov.:
31
AF XY:
AC XY:
37676
AN XY:
74238
show subpopulations
African (AFR)
AF:
AC:
16305
AN:
41406
American (AMR)
AF:
AC:
7715
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
1813
AN:
3470
East Asian (EAS)
AF:
AC:
2746
AN:
5154
South Asian (SAS)
AF:
AC:
3236
AN:
4810
European-Finnish (FIN)
AF:
AC:
5374
AN:
10530
Middle Eastern (MID)
AF:
AC:
175
AN:
294
European-Non Finnish (NFE)
AF:
AC:
38274
AN:
67940
Other (OTH)
AF:
AC:
1119
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1887
3774
5661
7548
9435
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
696
1392
2088
2784
3480
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2155
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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