chr14-52327516-T-C

Position:

• chr14-52327516-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_000956.4(PTGER2):​c.*62T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 1,328,124 control chromosomes in the GnomAD database, including 461,405 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 (46838 hom., cov: 32)
  • Exomes 𝑓: 0.83 (414567 hom.)
• Consequence: PTGER2 NM_000956.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• 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	Protein	UniProt
PTGER2	NM_000956.4	c.*62T>C		3_prime_UTR_variant	2/2	ENST00000245457.6	NP_000947.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGER2	ENST00000245457.6	c.*62T>C		3_prime_UTR_variant	2/2	1	NM_000956.4	ENSP00000245457	P1
PTGER2	ENST00000557436.1			downstream_gene_variant		3		ENSP00000450933

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118025 AN: 152016 Hom.: 46816 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: 0.589

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.794

GnomAD4 exome AF: 0.833 AC: 980022 AN: 1175990 Hom.: 414567 Cov.: 16 AF XY: 0.825 AC XY: 488373 AN XY: 591774

Gnomad4 AFR exome AF: 0.644

Gnomad4 AMR exome AF: 0.777

Gnomad4 ASJ exome AF: 0.858

Gnomad4 EAS exome AF: 0.593

Gnomad4 SAS exome AF: 0.549

Gnomad4 FIN exome AF: 0.795

Gnomad4 NFE exome AF: 0.877

Gnomad4 OTH exome AF: 0.812

GnomAD4 genome AF: 0.776 AC: 118093 AN: 152134 Hom.: 46838 Cov.: 32 AF XY: 0.767 AC XY: 57040 AN XY: 74376

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.792

Alfa AF: 0.856 Hom.: 50580

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	-0.37
CADD	Benign	14
DANN	Benign	0.91

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: rs708502; hg19: chr14-52794234;