rs6424414

Variant names:

• chr1-70989787-T-C
• rs6424414
• NM_198719.2:c.1078-15399A>G

Variant summary

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

The NM_198719.2(PTGER3):​c.1078-15399A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,936 control chromosomes in the GnomAD database, including 29,773 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 0.62 (29773 hom., cov: 31)
• Consequence: PTGER3 NM_198719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 13 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER3	NM_198719.2	c.1078-15399A>G		intron_variant	Intron 2 of 3	ENST00000306666.10	NP_942012.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000306666.10	c.1078-15399A>G		intron_variant	Intron 2 of 3	1	NM_198719.2	ENSP00000302313.5

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94676 AN: 151818 Hom.: 29762 Cov.: 31

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.623 AC: 94722 AN: 151936 Hom.: 29773 Cov.: 31 AF XY: 0.623 AC XY: 46270 AN XY: 74236

African (AFR) AF: 0.641 AC: 26525 AN: 41398

American (AMR) AF: 0.549 AC: 8379 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2662 AN: 5152

South Asian (SAS) AF: 0.609 AC: 2932 AN: 4814

European-Finnish (FIN) AF: 0.684 AC: 7209 AN: 10540

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42919 AN: 67988

Other (OTH) AF: 0.598 AC: 1264 AN: 2112

Alfa AF: 0.624 Hom.: 16627

Bravo AF: 0.612

Asia WGS AF: 0.594 AC: 2068 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.63
PhyloP100		-1.4
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: rs6424414; hg19: chr1-71455470; COSMIC: COSV60699661;