rs344782

Variant names:

• chr19-43668738-A-C
• rs344782
• NM_002659.4:c.56-1047T>G

Your query was ambiguous. Multiple possible variants found:

• chr19-43668738-A-C
• chr19-43668738-A-G
• chr19-43668738-A-T

Variant summary

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

The NM_002659.4(PLAUR):​c.56-1047T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 148,486 control chromosomes in the GnomAD database, including 20,864 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 0.53 (20864 hom., cov: 25)
• Consequence: PLAUR NM_002659.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 6 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.54 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.56-1047T>G		intron	N/A	NP_002650.1	Q03405-1
	PLAUR	NM_001005377.3		c.56-1047T>G		intron	N/A	NP_001005377.1	Q03405-3
	PLAUR	NM_001301037.2		c.56-1047T>G		intron	N/A	NP_001287966.1	M0R1I2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAUR	ENST00000340093.8	TSL:1 MANE Select	c.56-1047T>G		intron	N/A	ENSP00000339328.3	Q03405-1
	PLAUR	ENST00000221264.8	TSL:1	c.56-1047T>G		intron	N/A	ENSP00000221264.3	Q03405-3
	PLAUR	ENST00000601723.5	TSL:1	c.56-1047T>G		intron	N/A	ENSP00000471881.1	M0R1I2

Frequencies

GnomAD3 genomes AF: 0.533 AC: 79072 AN: 148364 Hom.: 20839 Cov.: 25

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.537

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.533 AC: 79154 AN: 148486 Hom.: 20864 Cov.: 25 AF XY: 0.533 AC XY: 38495 AN XY: 72256

African (AFR) AF: 0.521 AC: 20871 AN: 40026

American (AMR) AF: 0.546 AC: 8105 AN: 14834

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1544 AN: 3454

East Asian (EAS) AF: 0.465 AC: 2291 AN: 4928

South Asian (SAS) AF: 0.485 AC: 2276 AN: 4694

European-Finnish (FIN) AF: 0.576 AC: 5788 AN: 10056

Middle Eastern (MID) AF: 0.536 AC: 148 AN: 276

European-Non Finnish (NFE) AF: 0.544 AC: 36601 AN: 67256

Other (OTH) AF: 0.533 AC: 1102 AN: 2068

Alfa AF: 0.526 Hom.: 7251

Bravo AF: 0.523

Asia WGS AF: 0.475 AC: 1651 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.46
PhyloP100		-1.6
PromoterAI		0.028	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs344782; hg19: chr19-44172890; COSMIC: COSV55389076; COSMIC: COSV55389076;