rs17197

Variant names:

• chr14-52327663-G-A
• rs17197
• NM_000956.4:c.*209G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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]

PTGER2 Gene-Disease associations (from GenCC):

• asthma, nasal polyps, and aspirin intolerance

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000956.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER2	NM_000956.4	MANE Select	c.*209G>A		3_prime_UTR	Exon 2 of 2	NP_000947.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER2	ENST00000245457.6	TSL:1 MANE Select	c.*209G>A		3_prime_UTR	Exon 2 of 2	ENSP00000245457.5
	PTGER2	ENST00000557436.2	TSL:3	c.*209G>A		3_prime_UTR	Exon 3 of 3	ENSP00000450933.1

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

African (AFR) AF: 0.654 AC: 6430 AN: 9834

American (AMR) AF: 0.771 AC: 9400 AN: 12198

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 9856 AN: 11506

East Asian (EAS) AF: 0.593 AC: 15391 AN: 25962

South Asian (SAS) AF: 0.548 AC: 15378 AN: 28054

European-Finnish (FIN) AF: 0.796 AC: 18758 AN: 23578

Middle Eastern (MID) AF: 0.800 AC: 1306 AN: 1632

European-Non Finnish (NFE) AF: 0.873 AC: 190698 AN: 218324

Other (OTH) AF: 0.805 AC: 17118 AN: 21264

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

African (AFR) AF: 0.652 AC: 27011 AN: 41452

American (AMR) AF: 0.774 AC: 11839 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2973 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3055 AN: 5176

South Asian (SAS) AF: 0.533 AC: 2573 AN: 4826

European-Finnish (FIN) AF: 0.803 AC: 8489 AN: 10578

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59435 AN: 68012

Other (OTH) AF: 0.793 AC: 1676 AN: 2114

Alfa AF: 0.838 Hom.: 100339

Bravo AF: 0.772

Asia WGS AF: 0.618 AC: 2147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.020
DANN	Benign	0.38
PhyloP100		-3.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17197; hg19: chr14-52794381;