chr1-70909817-T-C

Variant names:

• chr1-70909817-T-C
• rs17541777
• ENST00000370931.7:c.*23+43946A>G

Variant summary

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

The NM_198714.2(PTGER3):​c.*23+43946A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,294 control chromosomes in the GnomAD database, including 1,321 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 0.11 (1321 hom., cov: 32)
• Consequence: PTGER3 NM_198714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 3 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 (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 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.*23+43946A>G		intron	N/A	NP_942007.1	P43115-1
	PTGER3	NM_198716.2		c.1104+43946A>G		intron	N/A	NP_942009.1	P43115-4
	PTGER3	NM_198717.2		c.1078-56958A>G		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.*23+43946A>G		intron	N/A	ENSP00000359969.3	P43115-1
	PTGER3	ENST00000460330.5	TSL:1	c.1104+43946A>G		intron	N/A	ENSP00000418073.1	P43115-4
	PTGER3	ENST00000628037.2	TSL:1	c.1078-56958A>G		intron	N/A	ENSP00000486617.1	P43115-3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17505 AN: 152176 Hom.: 1323 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.115 AC: 17499 AN: 152294 Hom.: 1321 Cov.: 32 AF XY: 0.111 AC XY: 8257 AN XY: 74468

African (AFR) AF: 0.0448 AC: 1863 AN: 41570

American (AMR) AF: 0.126 AC: 1924 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 833 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0501 AC: 242 AN: 4834

European-Finnish (FIN) AF: 0.0997 AC: 1058 AN: 10612

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11000 AN: 68004

Other (OTH) AF: 0.154 AC: 326 AN: 2112

Alfa AF: 0.151 Hom.: 2265

Bravo AF: 0.117

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.76
PhyloP100		-1.3
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: rs17541777; hg19: chr1-71375500;