rs12461917

Variant names:

• chr19-46614145-C-A
• rs12461917
• ENST00000789035.1:n.287+2809C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-46614145-C-A
• chr19-46614145-C-T

Variant summary

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

The ENST00000789035.1(ENSG00000302712):​n.287+2809C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,192 control chromosomes in the GnomAD database, including 2,070 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 0.15 (2070 hom., cov: 32)
• Consequence: ENSG00000302712 ENST00000789035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.476
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGIR	XR_243945.4	n.1097+47G>T		intron_variant	Intron 3 of 3
PTGIR	XR_430206.4	n.1097+47G>T		intron_variant	Intron 3 of 3
PTGIR	XR_935844.3	n.1097+47G>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302712	ENST00000789035.1	n.287+2809C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23438 AN: 152074 Hom.: 2072 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0926

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.154 AC: 23447 AN: 152192 Hom.: 2070 Cov.: 32 AF XY: 0.155 AC XY: 11519 AN XY: 74400

African (AFR) AF: 0.234 AC: 9709 AN: 41504

American (AMR) AF: 0.0923 AC: 1411 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5180

South Asian (SAS) AF: 0.228 AC: 1100 AN: 4830

European-Finnish (FIN) AF: 0.150 AC: 1593 AN: 10596

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8698 AN: 68000

Other (OTH) AF: 0.139 AC: 293 AN: 2114

Alfa AF: 0.124 Hom.: 816

Bravo AF: 0.151

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.61
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs12461917; hg19: chr19-47117402;