chr1-70960577-A-G

Position:

• chr1-70960577-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000356595.8(PTGER3):​c.1078-6788T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,128 control chromosomes in the GnomAD database, including 2,068 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 0.13 (2068 hom., cov: 32)
• Consequence: PTGER3 ENST00000356595.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER3	NM_001126044.2	c.1170-6788T>C		intron_variant
PTGER3	NM_198714.2	c.1170-6788T>C		intron_variant
PTGER3	NM_198716.2	c.1078-6788T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000356595.8	c.1078-6788T>C		intron_variant		1
PTGER3	ENST00000370931.7	c.1170-6788T>C		intron_variant		1		A1
PTGER3	ENST00000460330.5	c.1078-6788T>C		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20084 AN: 152010 Hom.: 2058 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0502

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.132 AC: 20127 AN: 152128 Hom.: 2068 Cov.: 32 AF XY: 0.128 AC XY: 9514 AN XY: 74378

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.0773

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0502

Gnomad4 NFE AF: 0.0892

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0981 Hom.: 1532

Bravo AF: 0.141

Asia WGS AF: 0.0310 AC: 107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs977214; hg19: chr1-71426260;