chr1-70865815-A-G

Variant names:

• chr1-70865815-A-G
• rs1409986
• ENST00000370931.7:c.*24-12956T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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-AS1 (HGNC:40481):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198714.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	NM_198714.2		c.*24-12956T>C		intron	N/A	NP_942007.1	P43115-1
	PTGER3	NM_198716.2		c.1105-12956T>C		intron	N/A	NP_942009.1	P43115-4
	PTGER3	NM_198717.2		c.1078-12956T>C		intron	N/A	NP_942010.1	P43115-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	ENST00000370931.7	TSL:1	c.*24-12956T>C		intron	N/A	ENSP00000359969.3	P43115-1
	PTGER3	ENST00000460330.5	TSL:1	c.1105-12956T>C		intron	N/A	ENSP00000418073.1	P43115-4
	PTGER3	ENST00000628037.2	TSL:1	c.1078-12956T>C		intron	N/A	ENSP00000486617.1	P43115-3

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

GnomAD2 exomes AF: 0.941 AC: 236063 AN: 250890 AF XY: 0.940

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 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

African (AFR) AF: 0.987 AC: 25873 AN: 26222

American (AMR) AF: 0.971 AC: 36178 AN: 37274

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 15090 AN: 16890

East Asian (EAS) AF: 1.00 AC: 16784 AN: 16786

South Asian (SAS) AF: 0.971 AC: 80758 AN: 83148

European-Finnish (FIN) AF: 0.890 AC: 28994 AN: 32576

Middle Eastern (MID) AF: 0.911 AC: 4047 AN: 4444

European-Non Finnish (NFE) AF: 0.917 AC: 871993 AN: 950580

Other (OTH) AF: 0.925 AC: 40605 AN: 43894

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

African (AFR) AF: 0.985 AC: 40900 AN: 41536

American (AMR) AF: 0.957 AC: 14631 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3119 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5156 AN: 5160

South Asian (SAS) AF: 0.974 AC: 4688 AN: 4814

European-Finnish (FIN) AF: 0.895 AC: 9471 AN: 10588

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62584 AN: 68014

Other (OTH) AF: 0.937 AC: 1978 AN: 2112

Alfa AF: 0.931 Hom.: 143678

Bravo AF: 0.950

Asia WGS AF: 0.984 AC: 3422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.066
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.61
PhyloP100		0.0080
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1409986; hg19: chr1-71331498;