rs1058720
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_000930.5(PLAT):c.501C>T(p.Asp167=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 1,599,912 control chromosomes in the GnomAD database, including 252,845 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.52 ( 20670 hom., cov: 34)
Exomes 𝑓: 0.57 ( 232175 hom. )
Consequence
PLAT
NM_000930.5 synonymous
NM_000930.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.266
Genes affected
PLAT (HGNC:9051): (plasminogen activator, tissue type) This gene encodes tissue-type plasminogen activator, a secreted serine protease that converts the proenzyme plasminogen to plasmin, a fibrinolytic enzyme. The encoded preproprotein is proteolytically processed by plasmin or trypsin to generate heavy and light chains. These chains associate via disulfide linkages to form the heterodimeric enzyme. This enzyme plays a role in cell migration and tissue remodeling. Increased enzymatic activity causes hyperfibrinolysis, which manifests as excessive bleeding, while decreased activity leads to hypofibrinolysis, which can result in thrombosis or embolism. Alternative splicing of this gene 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 8-42187436-G-A is Benign according to our data. Variant chr8-42187436-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.266 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLAT | NM_000930.5 | c.501C>T | p.Asp167= | synonymous_variant | 6/14 | ENST00000220809.9 | |
PLAT | NM_033011.4 | c.363C>T | p.Asp121= | synonymous_variant | 5/13 | ||
PLAT | NM_001319189.2 | c.364+470C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLAT | ENST00000220809.9 | c.501C>T | p.Asp167= | synonymous_variant | 6/14 | 1 | NM_000930.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.515 AC: 78404AN: 152110Hom.: 20674 Cov.: 34
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GnomAD3 exomes AF: 0.550 AC: 133028AN: 241960Hom.: 37016 AF XY: 0.553 AC XY: 72634AN XY: 131446
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GnomAD4 exome AF: 0.565 AC: 818148AN: 1447684Hom.: 232175 Cov.: 48 AF XY: 0.564 AC XY: 406534AN XY: 720290
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GnomAD4 genome ? AF: 0.515 AC: 78430AN: 152228Hom.: 20670 Cov.: 34 AF XY: 0.516 AC XY: 38410AN XY: 74420
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Not reported inComputational scores
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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