rs17197

chr14-52327663-G-A

Variant summary

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

The NM_000956.4(PTGER2):c.*209G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 504,474 control chromosomes in the GnomAD database, including 164,101 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 0.78 (46830 hom., cov: 32)
  • Exomes 𝑓: 0.81 (117271 hom.)
• Consequence: PTGER2 NM_000956.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.60

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER2	NM_000956.4	c.*209G>A		3_prime_UTR_variant	2/2	ENST00000245457.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER2	ENST00000245457.6	c.*209G>A		3_prime_UTR_variant	2/2	1	NM_000956.4	P1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118017 AN: 152004 Hom.: 46808 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.774

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.794

GnomAD4 exome AF: 0.807 AC: 284335 AN: 352352 Hom.: 117271 Cov.: 4 AF XY: 0.797 AC XY: 146873 AN XY: 184230

Gnomad4 AFR exome AF: 0.654

Gnomad4 AMR exome AF: 0.771

Gnomad4 ASJ exome AF: 0.857

Gnomad4 EAS exome AF: 0.593

Gnomad4 SAS exome AF: 0.548

Gnomad4 FIN exome AF: 0.796

Gnomad4 NFE exome AF: 0.873

Gnomad4 OTH exome AF: 0.805

GnomAD4 genome AF: 0.776 AC: 118085 AN: 152122 Hom.: 46830 Cov.: 32 AF XY: 0.767 AC XY: 57045 AN XY: 74366

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.793

Alfa AF: 0.850 Hom.: 73945

Bravo AF: 0.772

Asia WGS AF: 0.618 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.020
Dann	Benign	0.38

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: rs17197; hg19: chr14-52794381;