rs10815216

chr9-5420526-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018465.4(PLGRKT):c.81+11371T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,994 control chromosomes in the GnomAD database, including 7,252 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 0.31 (7252 hom., cov: 31)
• Consequence: PLGRKT NM_018465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

Genes affected

PLGRKT (HGNC:23633): (plasminogen receptor with a C-terminal lysine) Predicted to be involved in positive regulation of plasminogen activation. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLGRKT	NM_018465.4	c.81+11371T>G		intron_variant		ENST00000223864.7
PLGRKT	XM_005251510.6	c.81+11371T>G		intron_variant
PLGRKT	XM_011517960.3	c.81+11371T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLGRKT	ENST00000223864.7	c.81+11371T>G		intron_variant		1	NM_018465.4	P1
PLGRKT	ENST00000472145.5	n.288+11371T>G		intron_variant, non_coding_transcript_variant		2
PLGRKT	ENST00000473877.1	n.213+11371T>G		intron_variant, non_coding_transcript_variant		3
PLGRKT	ENST00000482696.5	n.292+11371T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46526 AN: 151876 Hom.: 7238 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.306 AC: 46569 AN: 151994 Hom.: 7252 Cov.: 31 AF XY: 0.304 AC XY: 22599 AN XY: 74302

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.314

Alfa AF: 0.312 Hom.: 1957

Bravo AF: 0.304

Asia WGS AF: 0.347 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.088
Dann	Benign	0.48

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

Other links and lift over

dbSNP: rs10815216; hg19: chr9-5420526;