ENST00000370931.7:c.*23+50080A>C

Variant names:

• chr1-70903683-T-G
• rs17482481
• ENST00000370931.7:c.*23+50080A>C

Variant summary

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

The ENST00000370931.7(PTGER3):​c.*23+50080A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,874 control chromosomes in the GnomAD database, including 6,973 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 0.30 (6973 hom., cov: 32)
• Consequence: PTGER3 ENST00000370931.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER3	NM_198714.2	c.*23+50080A>C		intron_variant	Intron 4 of 4		NP_942007.1
PTGER3	NM_198716.2	c.1104+50080A>C		intron_variant	Intron 3 of 3		NP_942009.1
PTGER3	NM_198717.2	c.1078-50824A>C		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.*23+50080A>C		intron_variant	Intron 4 of 4	1		ENSP00000359969.3
PTGER3	ENST00000460330.5	c.1104+50080A>C		intron_variant	Intron 3 of 3	1		ENSP00000418073.1
PTGER3	ENST00000628037.2	c.1078-50824A>C		intron_variant	Intron 2 of 2	1		ENSP00000486617.1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45074 AN: 151758 Hom.: 6960 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.297 AC: 45129 AN: 151874 Hom.: 6973 Cov.: 32 AF XY: 0.304 AC XY: 22550 AN XY: 74212

African (AFR) AF: 0.258 AC: 10686 AN: 41412

American (AMR) AF: 0.279 AC: 4262 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1975 AN: 5154

South Asian (SAS) AF: 0.454 AC: 2188 AN: 4816

European-Finnish (FIN) AF: 0.348 AC: 3656 AN: 10518

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20167 AN: 67934

Other (OTH) AF: 0.299 AC: 632 AN: 2114

Alfa AF: 0.299 Hom.: 886

Bravo AF: 0.286

Asia WGS AF: 0.428 AC: 1487 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.45
PhyloP100		-0.21
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: rs17482481; hg19: chr1-71369366;