chr1-70977467-T-C

Variant names:

• chr1-70977467-T-C
• rs909848
• NM_198719.2:c.1078-3079A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198718.2(PTGER3):​c.1078-23678A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 151,472 control chromosomes in the GnomAD database, including 28,752 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 0.61 (28752 hom., cov: 30)
• Consequence: PTGER3 NM_198718.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 11 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198718.2. 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_198719.2	MANE Select	c.1078-3079A>G		intron	N/A	NP_942012.1
	PTGER3	NM_198718.2		c.1078-23678A>G		intron	N/A	NP_942011.1
	PTGER3	NM_001126044.2		c.1078-3079A>G		intron	N/A	NP_001119516.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	ENST00000306666.10	TSL:1 MANE Select	c.1078-3079A>G		intron	N/A	ENSP00000302313.5
	PTGER3	ENST00000356595.8	TSL:1	c.1078-23678A>G		intron	N/A	ENSP00000349003.4
	PTGER3	ENST00000370931.7	TSL:1	c.1078-3079A>G		intron	N/A	ENSP00000359969.3

Frequencies

GnomAD3 genomes AF: 0.614 AC: 92963 AN: 151356 Hom.: 28736 Cov.: 30

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.644

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.614 AC: 93015 AN: 151472 Hom.: 28752 Cov.: 30 AF XY: 0.614 AC XY: 45425 AN XY: 73980

African (AFR) AF: 0.613 AC: 25271 AN: 41240

American (AMR) AF: 0.547 AC: 8321 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1998 AN: 3466

East Asian (EAS) AF: 0.510 AC: 2609 AN: 5114

South Asian (SAS) AF: 0.606 AC: 2920 AN: 4820

European-Finnish (FIN) AF: 0.682 AC: 7168 AN: 10510

Middle Eastern (MID) AF: 0.646 AC: 186 AN: 288

European-Non Finnish (NFE) AF: 0.629 AC: 42660 AN: 67808

Other (OTH) AF: 0.594 AC: 1252 AN: 2108

Alfa AF: 0.608 Hom.: 24183

Bravo AF: 0.602

Asia WGS AF: 0.587 AC: 2046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.2
DANN	Benign	0.85
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs909848; hg19: chr1-71443150;