rs959

chr1-70852578-T-C

Variant summary

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

The ENST00000370931.7(PTGER3):c.*305A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 509,536 control chromosomes in the GnomAD database, including 14,234 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 0.19 (3505 hom., cov: 32)
  • Exomes 𝑓: 0.23 (10729 hom.)
• Consequence: PTGER3 ENST00000370931.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

Genes affected

PTGER3 (HGNC:9595): (prostaglandin E receptor 3) The protein encoded by this gene is a member of the G-protein coupled receptor family. This protein is one of four receptors identified for prostaglandin E2 (PGE2). This receptor may have many biological functions, which involve digestion, nervous system, kidney reabsorption, and uterine contraction activities. Studies of the mouse counterpart suggest that this receptor may also mediate adrenocorticotropic hormone response as well as fever generation in response to exogenous and endogenous stimuli. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]

LOC102724572 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724572	XR_426711.4	n.422-2460T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000370931.7	c.*305A>G		3_prime_UTR_variant	5/5	1		A1
PTGER3	ENST00000460330.5	c.*261A>G		3_prime_UTR_variant	4/4	1		A2
PTGER3	ENST00000628037.2	c.*261A>G		3_prime_UTR_variant	3/3	1		P4

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29059 AN: 152040 Hom.: 3495 Cov.: 32

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.231 AC: 82417 AN: 357378 Hom.: 10729 Cov.: 3 AF XY: 0.236 AC XY: 44394 AN XY: 188082

Gnomad4 AFR exome AF: 0.0760

Gnomad4 AMR exome AF: 0.378

Gnomad4 ASJ exome AF: 0.193

Gnomad4 EAS exome AF: 0.384

Gnomad4 SAS exome AF: 0.310

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.217

Gnomad4 OTH exome AF: 0.224

GnomAD4 genome AF: 0.191 AC: 29078 AN: 152158 Hom.: 3505 Cov.: 32 AF XY: 0.193 AC XY: 14363 AN XY: 74384

Gnomad4 AFR AF: 0.0770

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.195

Alfa AF: 0.204 Hom.: 1235

Bravo AF: 0.203

Asia WGS AF: 0.333 AC: 1156 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.4
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs959; hg19: chr1-71318261;