rs470358
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002421.4(MMP1):c.105+17A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 1,545,902 control chromosomes in the GnomAD database, including 288,881 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.66 ( 33408 hom., cov: 32)
Exomes 𝑓: 0.60 ( 255473 hom. )
Consequence
MMP1
NM_002421.4 intron
NM_002421.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0610
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 11-102797971-T-C is Benign according to our data. Variant chr11-102797971-T-C is described in ClinVar as [Benign]. Clinvar id is 1235418.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MMP1 | NM_002421.4 | c.105+17A>G | intron_variant | ENST00000315274.7 | |||
WTAPP1 | NR_038390.1 | n.584-53T>C | intron_variant, non_coding_transcript_variant | ||||
MMP1 | NM_001145938.2 | c.-53+128A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MMP1 | ENST00000315274.7 | c.105+17A>G | intron_variant | 1 | NM_002421.4 | P1 | |||
WTAPP1 | ENST00000371455.7 | n.325-53T>C | intron_variant, non_coding_transcript_variant | 4 | |||||
WTAPP1 | ENST00000525739.6 | n.584-53T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
WTAPP1 | ENST00000544704.1 | n.345-53T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.656 AC: 99685AN: 151992Hom.: 33379 Cov.: 32
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GnomAD3 exomes AF: 0.602 AC: 145180AN: 240986Hom.: 44336 AF XY: 0.599 AC XY: 78087AN XY: 130290
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GnomAD4 exome AF: 0.603 AC: 840613AN: 1393792Hom.: 255473 Cov.: 21 AF XY: 0.602 AC XY: 419120AN XY: 696696
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GnomAD4 genome ? AF: 0.656 AC: 99766AN: 152110Hom.: 33408 Cov.: 32 AF XY: 0.652 AC XY: 48509AN XY: 74358
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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