rs1353411

Positions:

• chr14-52314383-G-A
• chr14-52314383-G-C

Variant summary

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

The NM_000956.4(PTGER2):​c.-166G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 779,840 control chromosomes in the GnomAD database, including 24,739 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 0.28 (6903 hom., cov: 32)
  • Exomes 𝑓: 0.21 (17836 hom.)
• Consequence: PTGER2 NM_000956.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER2	NM_000956.4	c.-166G>A		5_prime_UTR_variant	1/2	ENST00000245457.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER2	ENST00000245457.6	c.-166G>A		5_prime_UTR_variant	1/2	1	NM_000956.4	P1
PTGER2	ENST00000557436.1	c.-198G>A		5_prime_UTR_variant	1/3	3

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42002 AN: 151750 Hom.: 6887 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.266

GnomAD4 exome AF: 0.214 AC: 134337 AN: 627982 Hom.: 17836 Cov.: 8 AF XY: 0.215 AC XY: 65330 AN XY: 304406

Gnomad4 AFR exome AF: 0.364

Gnomad4 AMR exome AF: 0.395

Gnomad4 ASJ exome AF: 0.189

Gnomad4 EAS exome AF: 0.577

Gnomad4 SAS exome AF: 0.561

Gnomad4 FIN exome AF: 0.184

Gnomad4 NFE exome AF: 0.182

Gnomad4 OTH exome AF: 0.257

GnomAD4 genome AF: 0.277 AC: 42065 AN: 151858 Hom.: 6903 Cov.: 32 AF XY: 0.287 AC XY: 21337 AN XY: 74238

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.267

Alfa AF: 0.229 Hom.: 556

Bravo AF: 0.292

Asia WGS AF: 0.513 AC: 1785 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1353411; hg19: chr14-52781101;