1-70865815-A-T

Variant names:

• chr1-70865815-A-T
• rs1409986
• ENST00000370931.7:c.*24-12956T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_198714.2(PTGER3):​c.*24-12956T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PTGER3 NM_198714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• 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]

PTGER3-AS1 (HGNC:40481):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.006).

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.*24-12956T>A		intron	N/A	NP_942007.1	P43115-1
	PTGER3	NM_198716.2		c.1105-12956T>A		intron	N/A	NP_942009.1	P43115-4
	PTGER3	NM_198717.2		c.1078-12956T>A		intron	N/A	NP_942010.1	P43115-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	ENST00000370931.7	TSL:1	c.*24-12956T>A		intron	N/A	ENSP00000359969.3	P43115-1
	PTGER3	ENST00000460330.5	TSL:1	c.1105-12956T>A		intron	N/A	ENSP00000418073.1	P43115-4
	PTGER3	ENST00000628037.2	TSL:1	c.1078-12956T>A		intron	N/A	ENSP00000486617.1	P43115-3

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1212242 Hom.: 0 Cov.: 42 AF XY: 0.00 AC XY: 0 AN XY: 600984

African (AFR) AF: 0.00 AC: 0 AN: 26224

American (AMR) AF: 0.00 AC: 0 AN: 37276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16892

East Asian (EAS) AF: 0.00 AC: 0 AN: 16786

South Asian (SAS) AF: 0.00 AC: 0 AN: 83150

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32582

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4446

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 950976

Other (OTH) AF: 0.00 AC: 0 AN: 43910

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.52
PhyloP100		0.0080

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1409986; hg19: chr1-71331498;