NM_004771.4:c.812-1039G>A
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.812-1039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0879 in 152,164 control chromosomes in the GnomAD database, including 751 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 0.088 ( 751 hom., cov: 32)
Exomes 𝑓: 0.094 ( 0 hom. )
Consequence
MMP20
NM_004771.4 intron
NM_004771.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0270
Publications
3 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]
Genome browser will be placed here
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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0880 AC: 13380AN: 152014Hom.: 751 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
13380
AN:
152014
Hom.:
Cov.:
32
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:
GnomAD4 exome AF: 0.0938 AC: 3AN: 32Hom.: 0 Cov.: 0 AF XY: 0.0500 AC XY: 1AN XY: 20 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
32
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
20
show subpopulations
African (AFR)
AF:
AC:
0
AN:
2
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
AC:
0
AN:
2
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
3
AN:
26
Other (OTH)
AF:
AC:
0
AN:
2
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.408
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0879 AC: 13376AN: 152132Hom.: 751 Cov.: 32 AF XY: 0.0869 AC XY: 6461AN XY: 74356 show subpopulations
GnomAD4 genome
AF:
AC:
13376
AN:
152132
Hom.:
Cov.:
32
AF XY:
AC XY:
6461
AN XY:
74356
show subpopulations
African (AFR)
AF:
AC:
888
AN:
41518
American (AMR)
AF:
AC:
1108
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
344
AN:
3462
East Asian (EAS)
AF:
AC:
438
AN:
5166
South Asian (SAS)
AF:
AC:
380
AN:
4824
European-Finnish (FIN)
AF:
AC:
1388
AN:
10554
Middle Eastern (MID)
AF:
AC:
10
AN:
294
European-Non Finnish (NFE)
AF:
AC:
8536
AN:
68004
Other (OTH)
AF:
AC:
172
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
611
1221
1832
2442
3053
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
158
316
474
632
790
<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:
249
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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