rs1126510

Positions:

• chr19-46620526-A-G

Variant summary

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

The NM_000960.4(PTGIR):​c.*754T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 985,036 control chromosomes in the GnomAD database, including 61,628 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 0.31 (7563 hom., cov: 31)
  • Exomes 𝑓: 0.36 (54065 hom.)
• Consequence: PTGIR NM_000960.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGIR	NM_000960.4	c.*754T>C		3_prime_UTR_variant	3/3	ENST00000291294.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGIR	ENST00000291294.7	c.*754T>C		3_prime_UTR_variant	3/3	1	NM_000960.4	P1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46902 AN: 151732 Hom.: 7563 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.340

GnomAD4 exome AF: 0.359 AC: 299168 AN: 833186 Hom.: 54065 Cov.: 31 AF XY: 0.361 AC XY: 138762 AN XY: 384776

Gnomad4 AFR exome AF: 0.269

Gnomad4 AMR exome AF: 0.211

Gnomad4 ASJ exome AF: 0.454

Gnomad4 EAS exome AF: 0.0959

Gnomad4 SAS exome AF: 0.392

Gnomad4 FIN exome AF: 0.276

Gnomad4 NFE exome AF: 0.361

Gnomad4 OTH exome AF: 0.350

GnomAD4 genome AF: 0.309 AC: 46928 AN: 151850 Hom.: 7563 Cov.: 31 AF XY: 0.303 AC XY: 22483 AN XY: 74214

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.462

Gnomad4 EAS AF: 0.0854

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.338

Alfa AF: 0.328 Hom.: 4654

Bravo AF: 0.308

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.94
DANN	Benign	0.62

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: rs1126510; hg19: chr19-47123783;