chr1-70929000-T-C

Position:

• chr1-70929000-T-C

Variant summary

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

The NM_198714.2(PTGER3):​c.*23+24763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,134 control chromosomes in the GnomAD database, including 61,271 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 0.90 (61271 hom., cov: 30)
• Consequence: PTGER3 NM_198714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGER3	NM_198714.2	c.*23+24763A>G		intron_variant			NP_942007.1
PTGER3	NM_198716.2	c.1104+24763A>G		intron_variant			NP_942009.1
PTGER3	NM_198717.2	c.1078-76141A>G		intron_variant			NP_942010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000370931.7	c.*23+24763A>G		intron_variant		1		ENSP00000359969.3
PTGER3	ENST00000460330.5	c.1104+24763A>G		intron_variant		1		ENSP00000418073.1
PTGER3	ENST00000628037.2	c.1078-76141A>G		intron_variant		1		ENSP00000486617.1

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136186 AN: 152016 Hom.: 61202 Cov.: 30

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.904

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.896 AC: 136315 AN: 152134 Hom.: 61271 Cov.: 30 AF XY: 0.898 AC XY: 66758 AN XY: 74332

Gnomad4 AFR AF: 0.972

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.905

Alfa AF: 0.862 Hom.: 82931

Bravo AF: 0.902

Asia WGS AF: 0.919 AC: 3195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.7
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs578096; hg19: chr1-71394683;