Variant chr19-43648851-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_002659.4(PLAUR):c.*39G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0551 in 1,587,112 control chromosomes in the GnomAD database, including 4,595 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 0.11 ( 1550 hom., cov: 31)

Exomes 𝑓: 0.050 ( 3045 hom. )

Consequence

PLAUR
NM_002659.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.33

Variant links:

Genes affected

PLAUR (HGNC:9053): (plasminogen activator, urokinase receptor) This gene encodes the receptor for urokinase plasminogen activator and, given its role in localizing and promoting plasmin formation, likely influences many normal and pathological processes related to cell-surface plasminogen activation and localized degradation of the extracellular matrix. It binds both the proprotein and mature forms of urokinase plasminogen activator and permits the activation of the receptor-bound pro-enzyme by plasmin. The protein lacks transmembrane or cytoplasmic domains and may be anchored to the plasma membrane by a glycosyl-phosphatidylinositol (GPI) moiety following cleavage of the nascent polypeptide near its carboxy-terminus. However, a soluble protein is also produced in some cell types. Alternative splicing results in multiple transcript variants encoding different isoforms. The proprotein experiences several post-translational cleavage reactions that have not yet been fully defined. [provided by RefSeq, Jul 2008]

PLAUR links:

Genome browser will be placed here

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 = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLAUR	NM_002659.4 linkuse as main transcript	c.*39G>A		3_prime_UTR_variant	7/7	ENST00000340093.8	NP_002650.1	Q03405-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLAUR	ENST00000340093 linkuse as main transcript	c.*39G>A		3_prime_UTR_variant	7/7	1	NM_002659.4	ENSP00000339328.3		Q03405-1

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16089

AN:

152046

Hom.:

1539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0681

Gnomad ASJ

AF:

0.0706

Gnomad EAS

AF:

0.173

Gnomad SAS

AF:

0.0710

Gnomad FIN

AF:

0.0299

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.0383

Gnomad OTH

AF:

0.0998

GnomAD3 exomes

AF:

0.0692

AC:

16619

AN:

240046

Hom.:

1024

AF XY:

0.0666

AC XY:

8613

AN XY:

129346

show subpopulations

Gnomad AFR exome

AF:

0.252

Gnomad AMR exome

AF:

0.0431

Gnomad ASJ exome

AF:

0.0783

Gnomad EAS exome

AF:

0.178

Gnomad SAS exome

AF:

0.0722

Gnomad FIN exome

AF:

0.0299

Gnomad NFE exome

AF:

0.0384

Gnomad OTH exome

AF:

0.0647

GnomAD4 exome

AF:

0.0497

AC:

71369

AN:

1434948

Hom.:

3045

Cov.:

AF XY:

0.0505

AC XY:

35810

AN XY:

709810

show subpopulations

Gnomad4 AFR exome

AF:

0.255

Gnomad4 AMR exome

AF:

0.0464

Gnomad4 ASJ exome

AF:

0.0756

Gnomad4 EAS exome

AF:

0.170

Gnomad4 SAS exome

AF:

0.0736

Gnomad4 FIN exome

AF:

0.0311

Gnomad4 NFE exome

AF:

0.0365

Gnomad4 OTH exome

AF:

0.0677

GnomAD4 genome

AF:

0.106

AC:

16140

AN:

152164

Hom.:

1550

Cov.:

AF XY:

0.105

AC XY:

7834

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.250

Gnomad4 AMR

AF:

0.0681

Gnomad4 ASJ

AF:

0.0706

Gnomad4 EAS

AF:

0.174

Gnomad4 SAS

AF:

0.0704

Gnomad4 FIN

AF:

0.0299

Gnomad4 NFE

AF:

0.0383

Gnomad4 OTH

AF:

0.100

Alfa

AF:

0.0443

Hom.:

Bravo

AF:

0.116

Asia WGS

AF:

0.113

AC:

391

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

0.31

DANN

Benign

0.66

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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