9-5410624-T-C

Position:

• chr9-5410624-T-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+21273A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 152,260 control chromosomes in the GnomAD database, including 681 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 0.080 (681 hom., cov: 32)
• Consequence: PLGRKT NM_018465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

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]

PLGRKT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLGRKT	NM_018465.4	c.81+21273A>G		intron_variant		ENST00000223864.7	NP_060935.2
PLGRKT	XM_005251510.6	c.81+21273A>G		intron_variant			XP_005251567.1
PLGRKT	XM_011517960.3	c.81+21273A>G		intron_variant			XP_011516262.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLGRKT	ENST00000223864.7	c.81+21273A>G		intron_variant		1	NM_018465.4	ENSP00000223864.2
PLGRKT	ENST00000472145.5	n.288+21273A>G		intron_variant		2
PLGRKT	ENST00000473877.1	n.214-17975A>G		intron_variant		3
PLGRKT	ENST00000482696.5	n.292+21273A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0803 AC: 12221 AN: 152142 Hom.: 677 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0684

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0345

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.0804 AC: 12241 AN: 152260 Hom.: 681 Cov.: 32 AF XY: 0.0819 AC XY: 6099 AN XY: 74442

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.0682

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0345

Gnomad4 NFE AF: 0.0461

Gnomad4 OTH AF: 0.0913

Alfa AF: 0.0563 Hom.: 490

Bravo AF: 0.0852

Asia WGS AF: 0.179 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	12
DANN	Benign	0.60

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: rs1535453; hg19: chr9-5410624; COSMIC: COSV56352195;