Variant rs2020922 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000220809.9(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
ENST00000220809.9 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.245

Variant links:

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]

PLAT links:

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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	Effect	MANE	Protein
PLAT	NM_000930.5 linkuse as main transcript	c.1086-28A>T	intron_variant	ENST00000220809.9	NP_000921.1
PLAT	NM_001319189.2 linkuse as main transcript	c.819-28A>T	intron_variant		NP_001306118.1
PLAT	NM_033011.4 linkuse as main transcript	c.948-28A>T	intron_variant		NP_127509.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLAT	ENST00000220809.9 linkuse as main transcript	c.1086-28A>T		intron_variant		1	NM_000930.5	ENSP00000220809	P1	P00750-1

Frequencies

GnomAD3 genomes

AF:

0.780

AC:

118709

AN:

152140

Hom.:

47202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.949

Gnomad AMI

AF:

0.675

Gnomad AMR

AF:

0.698

Gnomad ASJ

AF:

0.645

Gnomad EAS

AF:

0.749

Gnomad SAS

AF:

0.807

Gnomad FIN

AF:

0.760

Gnomad MID

AF:

0.691

Gnomad NFE

AF:

0.709

Gnomad OTH

AF:

0.759

GnomAD3 exomes

AF:

0.735

AC:

184569

AN:

251108

Hom.:

68578

AF XY:

0.736

AC XY:

99822

AN XY:

135710

show subpopulations

Gnomad AFR exome

AF:

0.952

Gnomad AMR exome

AF:

0.667

Gnomad ASJ exome

AF:

0.638

Gnomad EAS exome

AF:

0.748

Gnomad SAS exome

AF:

0.798

Gnomad FIN exome

AF:

0.764

Gnomad NFE exome

AF:

0.710

Gnomad OTH exome

AF:

0.714

GnomAD4 exome

AF:

0.725

AC:

1058806

AN:

1461360

Hom.:

385133

Cov.:

AF XY:

0.725

AC XY:

527269

AN XY:

726974

show subpopulations

Gnomad4 AFR exome

AF:

0.954

Gnomad4 AMR exome

AF:

0.671

Gnomad4 ASJ exome

AF:

0.637

Gnomad4 EAS exome

AF:

0.739

Gnomad4 SAS exome

AF:

0.793

Gnomad4 FIN exome

AF:

0.762

Gnomad4 NFE exome

AF:

0.714

Gnomad4 OTH exome

AF:

0.740

GnomAD4 genome

AF:

0.780

AC:

118810

AN:

152258

Hom.:

47248

Cov.:

AF XY:

0.780

AC XY:

58073

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.949

Gnomad4 AMR

AF:

0.697

Gnomad4 ASJ

AF:

0.645

Gnomad4 EAS

AF:

0.748

Gnomad4 SAS

AF:

0.805

Gnomad4 FIN

AF:

0.760

Gnomad4 NFE

AF:

0.709

Gnomad4 OTH

AF:

0.756

Alfa

AF:

0.676

Hom.:

4110

Bravo

AF:

0.779

Asia WGS

AF:

0.796

AC:

2771

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.91

DANN

Benign

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over