rs1535454

Positions:

• chr9-5410723-C-T

Variant summary

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

The NM_018465.4(PLGRKT):​c.81+21174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,114 control chromosomes in the GnomAD database, including 445 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 0.067 (445 hom., cov: 32)
• Consequence: PLGRKT NM_018465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.88).
• 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+21174G>A		intron_variant		ENST00000223864.7	NP_060935.2
PLGRKT	XM_005251510.6	c.81+21174G>A		intron_variant			XP_005251567.1
PLGRKT	XM_011517960.3	c.81+21174G>A		intron_variant			XP_011516262.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLGRKT	ENST00000223864.7	c.81+21174G>A		intron_variant		1	NM_018465.4	ENSP00000223864	P1
PLGRKT	ENST00000472145.5	n.288+21174G>A		intron_variant, non_coding_transcript_variant		2
PLGRKT	ENST00000473877.1	n.214-18074G>A		intron_variant, non_coding_transcript_variant		3
PLGRKT	ENST00000482696.5	n.292+21174G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0673 AC: 10224 AN: 151996 Hom.: 444 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0345

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0673 AC: 10232 AN: 152114 Hom.: 445 Cov.: 32 AF XY: 0.0686 AC XY: 5100 AN XY: 74376

Gnomad4 AFR AF: 0.0880

Gnomad4 AMR AF: 0.0621

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0345

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.0819

Alfa AF: 0.0553 Hom.: 278

Bravo AF: 0.0702

Asia WGS AF: 0.176 AC: 612 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.49
DANN	Benign	0.76

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: rs1535454; hg19: chr9-5410723; COSMIC: COSV56352205;