NM_002659.4:c.311-1441T>C

Variant names:

• chr19-43658081-A-G
• rs4251864
• NM_002659.4:c.311-1441T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002659.4(PLAUR):​c.311-1441T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,684 control chromosomes in the GnomAD database, including 2,241 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 0.15 (2241 hom., cov: 32)
• Consequence: PLAUR NM_002659.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 9 publications found

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]

ENSG00000308028 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002659.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAUR	NM_002659.4	MANE Select	c.311-1441T>C		intron	N/A	NP_002650.1
	PLAUR	NM_001005377.3		c.311-1441T>C		intron	N/A	NP_001005377.1
	PLAUR	NM_001301037.2		c.311-1441T>C		intron	N/A	NP_001287966.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAUR	ENST00000340093.8	TSL:1 MANE Select	c.311-1441T>C		intron	N/A	ENSP00000339328.3
	PLAUR	ENST00000221264.8	TSL:1	c.311-1441T>C		intron	N/A	ENSP00000221264.3
	PLAUR	ENST00000601723.5	TSL:1	c.311-1441T>C		intron	N/A	ENSP00000471881.1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22700 AN: 151568 Hom.: 2234 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0794

Gnomad OTH AF: 0.136

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.150 AC: 22725 AN: 151684 Hom.: 2241 Cov.: 32 AF XY: 0.151 AC XY: 11194 AN XY: 74176

African (AFR) AF: 0.270 AC: 11078 AN: 41104

American (AMR) AF: 0.119 AC: 1823 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3468

East Asian (EAS) AF: 0.303 AC: 1566 AN: 5174

South Asian (SAS) AF: 0.127 AC: 611 AN: 4810

European-Finnish (FIN) AF: 0.141 AC: 1487 AN: 10564

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0794 AC: 5400 AN: 67982

Other (OTH) AF: 0.136 AC: 287 AN: 2106

Alfa AF: 0.109 Hom.: 1952

Bravo AF: 0.156

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.68
PhyloP100		0.63
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4251864; hg19: chr19-44162233;