9-5410624-T-C

Variant names:

• chr9-5410624-T-C
• rs1535453
• NM_018465.4:c.81+21273A>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+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
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018465.4. 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
	PLGRKT	NM_018465.4	MANE Select	c.81+21273A>G		intron	N/A	NP_060935.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLGRKT	ENST00000223864.7	TSL:1 MANE Select	c.81+21273A>G		intron	N/A	ENSP00000223864.2
	PLGRKT	ENST00000472145.5	TSL:2	n.288+21273A>G		intron	N/A
	PLGRKT	ENST00000473877.1	TSL:3	n.214-17975A>G		intron	N/A

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

African (AFR) AF: 0.132 AC: 5470 AN: 41522

American (AMR) AF: 0.0682 AC: 1044 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3472

East Asian (EAS) AF: 0.151 AC: 782 AN: 5192

South Asian (SAS) AF: 0.161 AC: 778 AN: 4826

European-Finnish (FIN) AF: 0.0345 AC: 366 AN: 10600

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0461 AC: 3133 AN: 68022

Other (OTH) AF: 0.0913 AC: 193 AN: 2114

Alfa AF: 0.0593 Hom.: 1218

Bravo AF: 0.0852

Asia WGS AF: 0.179 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	12
DANN	Benign	0.60
PhyloP100		1.4
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: rs1535453; hg19: chr9-5410624; COSMIC: COSV56352195;