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GeneBe

11-102578800-A-AAAAC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_004771.4(MMP20):​c.1351+238_1351+239insGTTT 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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.88
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 -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

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MMP20NM_004771.4 linkuse as main transcriptc.1351+238_1351+239insGTTT intron_variant ENST00000260228.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MMP20ENST00000260228.3 linkuse as main transcriptc.1351+238_1351+239insGTTT intron_variant 1 NM_004771.4 P1
MMP20ENST00000542305.1 linkuse as main transcriptn.249+238_249+239insGTTT intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.332
AC:
50236
AN:
151176
Hom.:
8673
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.332
Gnomad AMI
AF:
0.189
Gnomad AMR
AF:
0.399
Gnomad ASJ
AF:
0.235
Gnomad EAS
AF:
0.539
Gnomad SAS
AF:
0.323
Gnomad FIN
AF:
0.408
Gnomad MID
AF:
0.299
Gnomad NFE
AF:
0.298
Gnomad OTH
AF:
0.324
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.332
AC:
50244
AN:
151296
Hom.:
8669
Cov.:
0
AF XY:
0.339
AC XY:
25057
AN XY:
73936
show subpopulations
Gnomad4 AFR
AF:
0.332
Gnomad4 AMR
AF:
0.398
Gnomad4 ASJ
AF:
0.235
Gnomad4 EAS
AF:
0.539
Gnomad4 SAS
AF:
0.323
Gnomad4 FIN
AF:
0.408
Gnomad4 NFE
AF:
0.298
Gnomad4 OTH
AF:
0.327

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 testingGeneDxJun 19, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs35673489; hg19: chr11-102449531; API