rs1409986

Positions:

• chr1-70865815-A-G
• chr1-70865815-A-T

Variant summary

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

The NM_198714.2(PTGER3):​c.*24-12956T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 1,364,008 control chromosomes in the GnomAD database, including 586,137 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 0.94 (67913 hom., cov: 30)
  • Exomes 𝑓: 0.92 (518224 hom.)
• Consequence: PTGER3 NM_198714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

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]

PTGER3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGER3	NM_198714.2	c.*24-12956T>C		intron_variant			NP_942007.1
PTGER3	NM_198716.2	c.1105-12956T>C		intron_variant			NP_942009.1
PTGER3	NM_198717.2	c.1078-12956T>C		intron_variant			NP_942010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000370931.7	c.*24-12956T>C		intron_variant		1		ENSP00000359969.3
PTGER3	ENST00000460330.5	c.1105-12956T>C		intron_variant		1		ENSP00000418073.1
PTGER3	ENST00000628037.2	c.1078-12956T>C		intron_variant		1		ENSP00000486617.1

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143556 AN: 152076 Hom.: 67853 Cov.: 30

Gnomad AFR AF: 0.985

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.936

GnomAD3 exomes AF: 0.941 AC: 236063 AN: 250890 Hom.: 111197 AF XY: 0.940 AC XY: 127430 AN XY: 135560

Gnomad AFR exome AF: 0.986

Gnomad AMR exome AF: 0.970

Gnomad ASJ exome AF: 0.892

Gnomad EAS exome AF: 1.00

Gnomad SAS exome AF: 0.973

Gnomad FIN exome AF: 0.894

Gnomad NFE exome AF: 0.921

Gnomad OTH exome AF: 0.932

GnomAD4 exome AF: 0.924 AC: 1120322 AN: 1211814 Hom.: 518224 Cov.: 42 AF XY: 0.926 AC XY: 556363 AN XY: 600794

Gnomad4 AFR exome AF: 0.987

Gnomad4 AMR exome AF: 0.971

Gnomad4 ASJ exome AF: 0.893

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.971

Gnomad4 FIN exome AF: 0.890

Gnomad4 NFE exome AF: 0.917

Gnomad4 OTH exome AF: 0.925

GnomAD4 genome AF: 0.944 AC: 143676 AN: 152194 Hom.: 67913 Cov.: 30 AF XY: 0.945 AC XY: 70334 AN XY: 74396

Gnomad4 AFR AF: 0.985

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.974

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.920

Gnomad4 OTH AF: 0.937

Alfa AF: 0.928 Hom.: 108883

Bravo AF: 0.950

Asia WGS AF: 0.984 AC: 3422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409986; hg19: chr1-71331498;