rs569444
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002422.5(MMP3):c.1334-348C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 485,038 control chromosomes in the GnomAD database, including 4,440 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.10 ( 1229 hom., cov: 32)
Exomes 𝑓: 0.13 ( 3211 hom. )
Consequence
MMP3
NM_002422.5 intron
NM_002422.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.607
Genes affected
MMP3 (HGNC:7173): (matrix metallopeptidase 3) 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. This gene encodes an enzyme which degrades fibronectin, laminin, collagens III, IV, IX, and X, and cartilage proteoglycans. The enzyme is thought to be involved in wound repair, progression of atherosclerosis, and tumor initiation. The gene is part of a cluster of MMP genes which localize to chromosome 11q22.3. [provided by RefSeq, Jul 2008]
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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=-0.91).
BP6
?
Variant 11-102836574-G-A is Benign according to our data. Variant chr11-102836574-G-A is described in ClinVar as [Benign]. Clinvar id is 1263820.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP3 | NM_002422.5 | c.1334-348C>T | intron_variant | ENST00000299855.10 | |||
WTAPP1 | NR_038390.1 | n.2450G>A | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP3 | ENST00000299855.10 | c.1334-348C>T | intron_variant | 1 | NM_002422.5 | P1 | |||
MMP3 | ENST00000434103.1 | c.265-46C>T | intron_variant | 3 | |||||
WTAPP1 | ENST00000525739.6 | n.2450G>A | non_coding_transcript_exon_variant | 8/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.104 AC: 15855AN: 151982Hom.: 1229 Cov.: 32
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GnomAD3 exomes AF: 0.120 AC: 18070AN: 150284Hom.: 1438 AF XY: 0.119 AC XY: 9545AN XY: 80504
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GnomAD4 exome AF: 0.127 AC: 42184AN: 332938Hom.: 3211 Cov.: 0 AF XY: 0.124 AC XY: 23162AN XY: 187376
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GnomAD4 genome ? AF: 0.104 AC: 15855AN: 152100Hom.: 1229 Cov.: 32 AF XY: 0.108 AC XY: 8057AN XY: 74322
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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 submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at