rs7541092

Variant names:

• chr1-70896789-G-A
• rs7541092
• ENST00000370931.7:c.*24-43930C>T

Variant summary

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

The ENST00000370931.7(PTGER3):​c.*24-43930C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0864 in 152,178 control chromosomes in the GnomAD database, including 1,040 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 0.086 (1040 hom., cov: 32)
• Consequence: PTGER3 ENST00000370931.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 6 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]

ENSG00000235782 (HGNC:40481):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER3	NM_198714.2	c.*24-43930C>T		intron_variant	Intron 4 of 4		NP_942007.1
PTGER3	NM_198716.2	c.1105-43930C>T		intron_variant	Intron 3 of 3		NP_942009.1
PTGER3	NM_198717.2	c.1078-43930C>T		intron_variant	Intron 2 of 2		NP_942010.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000370931.7	c.*24-43930C>T		intron_variant	Intron 4 of 4	1		ENSP00000359969.3
PTGER3	ENST00000460330.5	c.1105-43930C>T		intron_variant	Intron 3 of 3	1		ENSP00000418073.1
PTGER3	ENST00000628037.2	c.1078-43930C>T		intron_variant	Intron 2 of 2	1		ENSP00000486617.1

Frequencies

GnomAD3 genomes AF: 0.0863 AC: 13128 AN: 152060 Hom.: 1040 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0585

Gnomad AMR AF: 0.0619

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.0835

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0254

Gnomad OTH AF: 0.0714

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

GnomAD4 genome AF: 0.0864 AC: 13154 AN: 152178 Hom.: 1040 Cov.: 32 AF XY: 0.0892 AC XY: 6635 AN XY: 74400

African (AFR) AF: 0.194 AC: 8051 AN: 41512

American (AMR) AF: 0.0623 AC: 952 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1192 AN: 5176

South Asian (SAS) AF: 0.0834 AC: 402 AN: 4820

European-Finnish (FIN) AF: 0.0552 AC: 586 AN: 10608

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0254 AC: 1724 AN: 67996

Other (OTH) AF: 0.0754 AC: 159 AN: 2110

Alfa AF: 0.0409 Hom.: 479

Bravo AF: 0.0934

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.39
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: rs7541092; hg19: chr1-71362472; COSMIC: COSV63387786;