Genetic Variant PTGER1:c.942+118G>A (chr19-14473261-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000955.3(PTGER1):c.942+118G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 1,470,470 control chromosomes in the GnomAD database, including 4,765 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 0.10 ( 2646 hom., cov: 32)

Exomes 𝑓: 0.011 ( 2119 hom. )

Consequence

PTGER1
NM_000955.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.657

Publications

2 publications found

Variant links:

Genes affected

PTGER1 (HGNC:9593): (prostaglandin E receptor 1) 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). Through a phosphatidylinositol-calcium second messenger system, G-Q proteins mediate this receptor's activity. Knockout studies in mice suggested a role of this receptor in mediating algesia and in regulation of blood pressure. Studies in mice also suggested that this gene may mediate adrenocorticotropic hormone response to bacterial endotoxin. [provided by RefSeq, Jul 2008]

PTGER1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000955.3. 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
	PTGER1	NM_000955.3	MANE Select	c.942+118G>A		intron	N/A	NP_000946.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PTGER1	ENST00000292513.4	TSL:1 MANE Select	c.942+118G>A	intron	N/A	ENSP00000292513.3	P34995
PTGER1	ENST00000883541.1		c.942+118G>A	intron	N/A	ENSP00000553600.1
PTGER1	ENST00000883542.1		c.942+118G>A	intron	N/A	ENSP00000553601.1

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15603

AN:

151946

Hom.:

2632

Cov.:

show subpopulations

Gnomad AFR

AF:

0.354

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0422

Gnomad ASJ

AF:

0.00720

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00248

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00200

Gnomad OTH

AF:

0.0798

GnomAD4 exome

AF:

0.0109

AC:

14334

AN:

1318408

Hom.:

2119

AF XY:

0.00964

AC XY:

6226

AN XY:

645908

show subpopulations

African (AFR)

AF:

0.369

AC:

10559

AN:

28592

American (AMR)

AF:

0.0261

AC:

707

AN:

27138

Ashkenazi Jewish (ASJ)

AF:

0.00981

AC:

206

AN:

21000

East Asian (EAS)

AF:

0.00

AC:

AN:

33996

South Asian (SAS)

AF:

0.00109

AC:

AN:

68940

European-Finnish (FIN)

AF:

0.000380

AC:

AN:

31552

Middle Eastern (MID)

AF:

0.0235

AC:

102

AN:

4332

European-Non Finnish (NFE)

AF:

0.00118

AC:

1233

AN:

1047920

Other (OTH)

AF:

0.0262

AC:

1440

AN:

54938

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

501

1002

1502

2003

2504

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

324

648

972

1296

1620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.103

AC:

15646

AN:

152062

Hom.:

2646

Cov.:

AF XY:

0.0997

AC XY:

7414

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.354

AC:

14656

AN:

41380

American (AMR)

AF:

0.0420

AC:

643

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00720

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5172

South Asian (SAS)

AF:

0.00166

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.000283

AC:

AN:

10612

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00199

AC:

135

AN:

67986

Other (OTH)

AF:

0.0790

AC:

167

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

479

959

1438

1918

2397

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0362

Hom.:

122

Bravo

AF:

0.118

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.5

(source)

DANN

Benign

0.71

PhyloP100

-0.66

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over