rs2020922
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000930.5(PLAT):c.1086-28A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 1,613,618 control chromosomes in the GnomAD database, including 432,381 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 0.78 ( 47248 hom., cov: 34)
Exomes 𝑓: 0.72 ( 385133 hom. )
Consequence
PLAT
NM_000930.5 intron
NM_000930.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.245
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLAT | NM_000930.5 | c.1086-28A>T | intron_variant | ENST00000220809.9 | |||
PLAT | NM_001319189.2 | c.819-28A>T | intron_variant | ||||
PLAT | NM_033011.4 | c.948-28A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLAT | ENST00000220809.9 | c.1086-28A>T | intron_variant | 1 | NM_000930.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.780 AC: 118709AN: 152140Hom.: 47202 Cov.: 34
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GnomAD3 exomes AF: 0.735 AC: 184569AN: 251108Hom.: 68578 AF XY: 0.736 AC XY: 99822AN XY: 135710
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GnomAD4 exome AF: 0.725 AC: 1058806AN: 1461360Hom.: 385133 Cov.: 48 AF XY: 0.725 AC XY: 527269AN XY: 726974
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GnomAD4 genome ? AF: 0.780 AC: 118810AN: 152258Hom.: 47248 Cov.: 34 AF XY: 0.780 AC XY: 58073AN XY: 74424
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ClinVar
Not reported inComputational 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