chr9-5420526-A-C

Variant names:

• chr9-5420526-A-C
• rs10815216
• NM_018465.4:c.81+11371T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PLGRKT	NM_018465.4	c.81+11371T>G		intron_variant	Intron 3 of 5	ENST00000223864.7	NP_060935.2
PLGRKT	XM_005251510.6	c.81+11371T>G		intron_variant	Intron 3 of 5		XP_005251567.1
PLGRKT	XM_011517960.3	c.81+11371T>G		intron_variant	Intron 3 of 5		XP_011516262.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLGRKT	ENST00000223864.7	c.81+11371T>G		intron_variant	Intron 3 of 5	1	NM_018465.4	ENSP00000223864.2
PLGRKT	ENST00000472145.5	n.288+11371T>G		intron_variant	Intron 3 of 3	2
PLGRKT	ENST00000473877.1	n.213+11371T>G		intron_variant	Intron 2 of 2	3
PLGRKT	ENST00000482696.5	n.292+11371T>G		intron_variant	Intron 3 of 4	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

African (AFR) AF: 0.270 AC: 11177 AN: 41466

American (AMR) AF: 0.306 AC: 4669 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3470

East Asian (EAS) AF: 0.174 AC: 898 AN: 5172

South Asian (SAS) AF: 0.412 AC: 1984 AN: 4810

European-Finnish (FIN) AF: 0.274 AC: 2896 AN: 10566

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22334 AN: 67930

Other (OTH) AF: 0.314 AC: 664 AN: 2112

Alfa AF: 0.319 Hom.: 12521

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
PhyloP100		-2.1
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: rs10815216; hg19: chr9-5420526;