1-70852578-T-C

Variant names:

• chr1-70852578-T-C
• rs959
• ENST00000370931.7:c.*305A>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.*305A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 509,536 control chromosomes in the GnomAD database, including 14,234 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 0.19 (3505 hom., cov: 32)
  • Exomes 𝑓: 0.23 (10729 hom.)
• Consequence: PTGER3 NM_198714.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100
• Publications: 22 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):

LOC102724572 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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.*305A>G		3_prime_UTR	Exon 5 of 5	NP_942007.1	P43115-1
	PTGER3	NM_198716.2		c.*261A>G		3_prime_UTR	Exon 4 of 4	NP_942009.1	P43115-4
	PTGER3	NM_198717.2		c.*261A>G		3_prime_UTR	Exon 3 of 3	NP_942010.1	P43115-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	ENST00000370931.7	TSL:1	c.*305A>G		3_prime_UTR	Exon 5 of 5	ENSP00000359969.3	P43115-1
	PTGER3	ENST00000460330.5	TSL:1	c.*261A>G		3_prime_UTR	Exon 4 of 4	ENSP00000418073.1	P43115-4
	PTGER3	ENST00000628037.2	TSL:1	c.*261A>G		3_prime_UTR	Exon 3 of 3	ENSP00000486617.1	P43115-3

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29059 AN: 152040 Hom.: 3495 Cov.: 32

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.231 AC: 82417 AN: 357378 Hom.: 10729 Cov.: 3 AF XY: 0.236 AC XY: 44394 AN XY: 188082

African (AFR) AF: 0.0760 AC: 657 AN: 8642

American (AMR) AF: 0.378 AC: 3974 AN: 10506

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 2205 AN: 11452

East Asian (EAS) AF: 0.384 AC: 9206 AN: 23972

South Asian (SAS) AF: 0.310 AC: 9410 AN: 30318

European-Finnish (FIN) AF: 0.133 AC: 3549 AN: 26628

Middle Eastern (MID) AF: 0.180 AC: 302 AN: 1674

European-Non Finnish (NFE) AF: 0.217 AC: 48363 AN: 222976

Other (OTH) AF: 0.224 AC: 4751 AN: 21210

GnomAD4 genome AF: 0.191 AC: 29078 AN: 152158 Hom.: 3505 Cov.: 32 AF XY: 0.193 AC XY: 14363 AN XY: 74384

African (AFR) AF: 0.0770 AC: 3200 AN: 41532

American (AMR) AF: 0.338 AC: 5167 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 648 AN: 3472

East Asian (EAS) AF: 0.390 AC: 2015 AN: 5172

South Asian (SAS) AF: 0.318 AC: 1536 AN: 4828

European-Finnish (FIN) AF: 0.116 AC: 1226 AN: 10580

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14598 AN: 67982

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.210 Hom.: 6488

Bravo AF: 0.203

Asia WGS AF: 0.333 AC: 1156 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		-0.010
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: rs959; hg19: chr1-71318261;