rs3740938
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The ENST00000236826.8(MMP8):c.873C>T(p.Leu291=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0738 in 1,600,928 control chromosomes in the GnomAD database, including 5,870 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 0.067 ( 532 hom., cov: 30)
Exomes 𝑓: 0.074 ( 5338 hom. )
Consequence
MMP8
ENST00000236826.8 synonymous
ENST00000236826.8 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0700
Genes affected
MMP8 (HGNC:7175): (matrix metallopeptidase 8) This gene encodes a member of the matrix metalloproteinase (MMP) family of proteins. These proteins are involved in the breakdown of extracellular matrix in embryonic development, reproduction, and tissue remodeling, as well as in disease processes, such as arthritis and metastasis. Proteolysis at different sites on this protein results in multiple active forms of the enzyme with distinct N-termini. This protein functions in the degradation of type I, II and III collagens. The gene is part of a cluster of MMP genes which localize to chromosome 11q22.3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP7
Synonymous conserved (PhyloP=-0.07 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMP8 | NM_002424.3 | c.873C>T | p.Leu291= | synonymous_variant | 6/10 | ENST00000236826.8 | NP_002415.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MMP8 | ENST00000236826.8 | c.873C>T | p.Leu291= | synonymous_variant | 6/10 | 1 | NM_002424.3 | ENSP00000236826 | P1 | |
MMP8 | ENST00000438475.2 | c.801C>T | p.Leu267= | synonymous_variant | 6/9 | 5 | ENSP00000401004 | |||
MMP8 | ENST00000528662.6 | c.*850C>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/12 | 5 | ENSP00000431431 |
Frequencies
GnomAD3 genomes AF: 0.0674 AC: 10159AN: 150710Hom.: 523 Cov.: 30
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GnomAD3 exomes AF: 0.0973 AC: 24250AN: 249108Hom.: 1712 AF XY: 0.0973 AC XY: 13109AN XY: 134668
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GnomAD4 exome AF: 0.0745 AC: 107987AN: 1450102Hom.: 5338 Cov.: 31 AF XY: 0.0764 AC XY: 55116AN XY: 721526
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GnomAD4 genome AF: 0.0675 AC: 10179AN: 150826Hom.: 532 Cov.: 30 AF XY: 0.0706 AC XY: 5200AN XY: 73610
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ClinVar
Not reported inComputational scores
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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