rs11083840

Variant names:

• chr19-46616653-T-G
• rs11083840
• ENST00000789035.1:n.288-4468T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789035.1(ENSG00000302712):​n.288-4468T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,898 control chromosomes in the GnomAD database, including 15,168 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 0.44 (15168 hom., cov: 31)
• Consequence: ENSG00000302712 ENST00000789035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 42 publications found

Genes affected

ENSG00000302712 (HGNC:):

PTGIR (HGNC:9602): (prostaglandin I2 receptor) The protein encoded by this gene is a member of the G-protein coupled receptor family 1 and has been shown to be a receptor for prostacyclin. Prostacyclin, the major product of cyclooxygenase in macrovascular endothelium, elicits a potent vasodilation and inhibition of platelet aggregation through binding to this receptor. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789035.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302712	ENST00000789035.1		n.288-4468T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66715 AN: 151782 Hom.: 15138 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.440 AC: 66809 AN: 151898 Hom.: 15168 Cov.: 31 AF XY: 0.436 AC XY: 32392 AN XY: 74244

African (AFR) AF: 0.551 AC: 22796 AN: 41396

American (AMR) AF: 0.381 AC: 5807 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1691 AN: 3468

East Asian (EAS) AF: 0.397 AC: 2050 AN: 5158

South Asian (SAS) AF: 0.499 AC: 2403 AN: 4818

European-Finnish (FIN) AF: 0.318 AC: 3351 AN: 10552

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27258 AN: 67934

Other (OTH) AF: 0.469 AC: 988 AN: 2108

Alfa AF: 0.420 Hom.: 22474

Bravo AF: 0.450

Asia WGS AF: 0.456 AC: 1588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		0.043

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11083840; hg19: chr19-47119910;