XR_243945.4:n.874-2361T>C

Variant names:

• chr19-46616776-A-G
• rs11083841
• XR_243945.4:n.874-2361T>C

Variant summary

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

The XR_243945.4(PTGIR):​n.874-2361T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,110 control chromosomes in the GnomAD database, including 5,600 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 0.25 (5600 hom., cov: 32)
• Consequence: PTGIR XR_243945.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380

Genes affected

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

Verdict is Benign. Variant got -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 = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGIR	XR_243945.4	n.874-2361T>C		intron_variant	Intron 2 of 3
PTGIR	XR_430206.4	n.874-2361T>C		intron_variant	Intron 2 of 3
PTGIR	XR_935844.3	n.874-2361T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.250 AC: 38068 AN: 151992 Hom.: 5590 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.251 AC: 38115 AN: 152110 Hom.: 5600 Cov.: 32 AF XY: 0.256 AC XY: 19003 AN XY: 74340

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.244

Alfa AF: 0.199 Hom.: 2004

Bravo AF: 0.256

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11083841; hg19: chr19-47120033;