NM_002421.4:c.782-21T>C
Variant names:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002421.4(MMP1):c.782-21T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 1,611,958 control chromosomes in the GnomAD database, including 715,025 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.95 ( 68669 hom., cov: 33)
Exomes 𝑓: 0.94 ( 646356 hom. )
Consequence
MMP1
NM_002421.4 intron
NM_002421.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.366
Genes affected
MMP1 (HGNC:7155): (matrix metallopeptidase 1) This gene encodes a member of the peptidase M10 family of matrix metalloproteinases (MMPs). Proteins in this 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. The encoded preproprotein is proteolytically processed to generate the mature protease. This secreted protease breaks down the interstitial collagens, including types I, II, and III. The gene is part of a cluster of MMP genes on chromosome 11. Mutations in this gene are associated with chronic obstructive pulmonary disease (COPD). Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 11-102795312-A-G is Benign according to our data. Variant chr11-102795312-A-G is described in ClinVar as [Benign]. Clinvar id is 1281805.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMP1 | NM_002421.4 | c.782-21T>C | intron_variant | Intron 5 of 9 | ENST00000315274.7 | NP_002412.1 | ||
MMP1 | NM_001145938.2 | c.584-21T>C | intron_variant | Intron 5 of 9 | NP_001139410.1 | |||
WTAPP1 | NR_038390.1 | n.583+88A>G | intron_variant | Intron 3 of 7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MMP1 | ENST00000315274.7 | c.782-21T>C | intron_variant | Intron 5 of 9 | 1 | NM_002421.4 | ENSP00000322788.6 | |||
WTAPP1 | ENST00000371455.7 | n.325-2712A>G | intron_variant | Intron 2 of 4 | 4 | |||||
WTAPP1 | ENST00000525739.6 | n.583+88A>G | intron_variant | Intron 3 of 7 | 2 | |||||
WTAPP1 | ENST00000544704.1 | n.345-2712A>G | intron_variant | Intron 1 of 3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.949 AC: 144395AN: 152172Hom.: 68611 Cov.: 33
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GnomAD3 exomes AF: 0.924 AC: 230705AN: 249776Hom.: 106860 AF XY: 0.925 AC XY: 124945AN XY: 135022
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GnomAD4 exome AF: 0.941 AC: 1372997AN: 1459668Hom.: 646356 Cov.: 34 AF XY: 0.940 AC XY: 682378AN XY: 726276
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GnomAD4 genome AF: 0.949 AC: 144512AN: 152290Hom.: 68669 Cov.: 33 AF XY: 0.945 AC XY: 70395AN XY: 74462
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Nov 12, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at