rs12587410

Positions:

• chr14-52323817-C-T

Variant summary

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

The NM_000956.4(PTGER2):​c.844-3404C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 152,214 control chromosomes in the GnomAD database, including 576 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 0.073 (576 hom., cov: 32)
• Consequence: PTGER2 NM_000956.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401

Genes affected

PTGER2 (HGNC:9594): (prostaglandin E receptor 2) This gene encodes a receptor for prostaglandin E2, a metabolite of arachidonic acid which has different biologic activities in a wide range of tissues. Mutations in this gene are associated with aspirin-induced susceptibility to asthma. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER2	NM_000956.4	c.844-3404C>T		intron_variant		ENST00000245457.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER2	ENST00000245457.6	c.844-3404C>T		intron_variant		1	NM_000956.4	P1
PTGER2	ENST00000557436.1	c.79-3404C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0733 AC: 11153 AN: 152096 Hom.: 572 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.0475

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.0286

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0331

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0735 AC: 11181 AN: 152214 Hom.: 576 Cov.: 32 AF XY: 0.0750 AC XY: 5581 AN XY: 74430

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0804

Gnomad4 ASJ AF: 0.0475

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0923

Gnomad4 FIN AF: 0.0286

Gnomad4 NFE AF: 0.0331

Gnomad4 OTH AF: 0.0672

Alfa AF: 0.0551 Hom.: 58

Bravo AF: 0.0801

Asia WGS AF: 0.139 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.53

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: rs12587410; hg19: chr14-52790535;