Genetic Variant ENST00000356595.8:c.1185delC (chr1-70952978-TG-T) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The ENST00000356595.8(PTGER3):c.1185delC(p.Asn395LysfsTer9) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00782 in 1,613,250 control chromosomes in the GnomAD database, including 68 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0057 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0080 ( 64 hom. )

Consequence

PTGER3
ENST00000356595.8 frameshift

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.531

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP6

Variant 1-70952978-TG-T is Benign according to our data. Variant chr1-70952978-TG-T is described in ClinVar as [Likely_benign]. Clinvar id is 770488.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	Protein	UniProt
PTGER3	NM_198718.2 link	c.1185delC	p.Asn395LysfsTer9	frameshift_variant	Exon 4 of 4	NP_942011.1	P43115-5O00325
PTGER3	NM_001126044.2 link	c.*104delC		3_prime_UTR_variant	Exon 5 of 5	NP_001119516.1	P43115-1
PTGER3	NM_198714.2 link	c.*23+784delC		intron_variant	Intron 4 of 4	NP_942007.1	P43115-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	Protein	UniProt
PTGER3	ENST00000356595.8 link	c.1185delC	p.Asn395LysfsTer9	frameshift_variant	Exon 4 of 4	1	ENSP00000349003.4	P43115-5
PTGER3	ENST00000370931.7 link	c.*23+784delC		intron_variant	Intron 4 of 4	1	ENSP00000359969.3	P43115-1
PTGER3	ENST00000460330.5 link	c.1104+784delC		intron_variant	Intron 3 of 3	1	ENSP00000418073.1	P43115-4

Frequencies

GnomAD3 genomes

AF:

0.00569

AC:

865

AN:

152146

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00113

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00518

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00866

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00901

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00541

AC:

1351

AN:

249840

Hom.:

AF XY:

0.00546

AC XY:

738

AN XY:

135190

show subpopulations

Gnomad AFR exome

AF:

0.00117

Gnomad AMR exome

AF:

0.00310

Gnomad ASJ exome

AF:

0.00328

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000817

Gnomad FIN exome

AF:

0.00911

Gnomad NFE exome

AF:

0.00834

Gnomad OTH exome

AF:

0.00556

GnomAD4 exome

AF:

0.00804

AC:

11749

AN:

1460986

Hom.:

Cov.:

AF XY:

0.00786

AC XY:

5714

AN XY:

726816

show subpopulations

Gnomad4 AFR exome

AF:

0.00114

Gnomad4 AMR exome

AF:

0.00309

Gnomad4 ASJ exome

AF:

0.00356

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00106

Gnomad4 FIN exome

AF:

0.00847

Gnomad4 NFE exome

AF:

0.00947

Gnomad4 OTH exome

AF:

0.00640

GnomAD4 genome

AF:

0.00568

AC:

865

AN:

152264

Hom.:

Cov.:

AF XY:

0.00545

AC XY:

406

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00113

Gnomad4 AMR

AF:

0.00517

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.00866

Gnomad4 NFE

AF:

0.00901

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00647

Hom.:

Bravo

AF:

0.00527

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00942

EpiControl

AF:

0.00884

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Oct 30, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over