NM_002658.6:c.369-87G>A

Variant names:

• chr10-73913203-G-A
• rs2227562
• NM_002658.6:c.369-87G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_002658.6(PLAU):​c.369-87G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 1,567,112 control chromosomes in the GnomAD database, including 21,148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.13 (1620 hom., cov: 32)
  • Exomes 𝑓: 0.16 (19528 hom.)
• Consequence: PLAU NM_002658.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.00500
• Publications: 25 publications found

Genes affected

PLAU (HGNC:9052): (plasminogen activator, urokinase) This gene encodes a secreted serine protease that converts plasminogen to plasmin. The encoded preproprotein is proteolytically processed to generate A and B polypeptide chains. These chains associate via a single disulfide bond to form the catalytically inactive high molecular weight urokinase-type plasminogen activator (HMW-uPA). HMW-uPA can be further processed into the catalytically active low molecular weight urokinase-type plasminogen activator (LMW-uPA). This low molecular weight form does not bind to the urokinase-type plasminogen activator receptor. Mutations in this gene may be associated with Quebec platelet disorder and late-onset Alzheimer's disease. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Jan 2016]

C10orf55 (HGNC:31008): (chromosome 10 putative open reading frame 55) Enables identical protein binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 10-73913203-G-A is Benign according to our data. Variant chr10-73913203-G-A is described in ClinVar as Benign. ClinVar VariationId is 1295119.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002658.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAU	NM_002658.6	MANE Select	c.369-87G>A		intron	N/A	NP_002649.2
	PLAU	NM_001441154.1		c.369-87G>A		intron	N/A	NP_001428083.1
	PLAU	NM_001441155.1		c.369-87G>A		intron	N/A	NP_001428084.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLAU	ENST00000372764.4	TSL:1 MANE Select	c.369-87G>A		intron	N/A	ENSP00000361850.3
	C10orf55	ENST00000409178.5	TSL:1	n.269-128C>T		intron	N/A
	PLAU	ENST00000446342.5	TSL:2	c.318-87G>A		intron	N/A	ENSP00000388474.1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20196 AN: 152040 Hom.: 1621 Cov.: 32

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.159 AC: 224800 AN: 1414954 Hom.: 19528 Cov.: 24 AF XY: 0.162 AC XY: 114560 AN XY: 705158

African (AFR) AF: 0.0704 AC: 2291 AN: 32548

American (AMR) AF: 0.0944 AC: 4132 AN: 43786

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 6688 AN: 24852

East Asian (EAS) AF: 0.321 AC: 12654 AN: 39444

South Asian (SAS) AF: 0.239 AC: 20053 AN: 83870

European-Finnish (FIN) AF: 0.152 AC: 8056 AN: 52890

Middle Eastern (MID) AF: 0.174 AC: 979 AN: 5624

European-Non Finnish (NFE) AF: 0.149 AC: 160259 AN: 1073228

Other (OTH) AF: 0.165 AC: 9688 AN: 58712

GnomAD4 genome AF: 0.133 AC: 20194 AN: 152158 Hom.: 1620 Cov.: 32 AF XY: 0.133 AC XY: 9884 AN XY: 74382

African (AFR) AF: 0.0707 AC: 2937 AN: 41536

American (AMR) AF: 0.0904 AC: 1382 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 914 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1585 AN: 5154

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4816

European-Finnish (FIN) AF: 0.143 AC: 1515 AN: 10588

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10251 AN: 67984

Other (OTH) AF: 0.123 AC: 259 AN: 2114

Alfa AF: 0.149 Hom.: 6006

Bravo AF: 0.127

Asia WGS AF: 0.243 AC: 848 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Jun 20, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.38
PhyloP100		-0.0050
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: rs2227562; hg19: chr10-75672961; COSMIC: COSV65641915; COSMIC: COSV65641915;