dbSNP rs16870224: PTGER4:c.*460G>A (chr5-40692838-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_000958.3(PTGER4):c.*460G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 985,214 control chromosomes in the GnomAD database, including 6,500 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 0.099 ( 945 hom., cov: 32)

Exomes 𝑓: 0.11 ( 5555 hom. )

Consequence

PTGER4
NM_000958.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.348

Publications

14 publications found

Variant links:

Genes affected

PTGER4 (HGNC:9596): (prostaglandin E receptor 4) 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 can activate T-cell factor signaling. It has been shown to mediate PGE2 induced expression of early growth response 1 (EGR1), regulate the level and stability of cyclooxygenase-2 mRNA, and lead to the phosphorylation of glycogen synthase kinase-3. Knockout studies in mice suggest that this receptor may be involved in the neonatal adaptation of circulatory system, osteoporosis, as well as initiation of skin immune responses. [provided by RefSeq, Jul 2008]

PTGER4 links:

TTC33 (HGNC:29959): (tetratricopeptide repeat domain 33)

TTC33 links:

Genome browser will be placed here

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=-0.49).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER4	NM_000958.3 link	c.*460G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000302472.4	NP_000949.1	P35408A0PJF5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PTGER4	ENST00000302472.4 link	c.*460G>A	3_prime_UTR_variant	Exon 3 of 3	1	NM_000958.3	ENSP00000302846.3	P35408
TTC33	ENST00000637375.1 link	c.221+53960C>T	intron_variant	Intron 2 of 2	5		ENSP00000490134.1	A0A1B0GUJ4
TTC33	ENST00000636863.1 link	c.221+53960C>T	intron_variant	Intron 2 of 3	5		ENSP00000490389.1	A0A1B0GV67
TTC33	ENST00000636106.1 link	c.221+53960C>T	intron_variant	Intron 2 of 2	5		ENSP00000490018.1	A0A1B0GU95

Frequencies

GnomAD3 genomes

AF:

0.0991

AC:

15050

AN:

151910

Hom.:

944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0269

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.0852

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.114

AC:

94982

AN:

833186

Hom.:

5555

Cov.:

AF XY:

0.114

AC XY:

43908

AN XY:

384914

show subpopulations

African (AFR)

AF:

0.0193

AC:

304

AN:

15758

American (AMR)

AF:

0.130

AC:

144

AN:

1106

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

911

AN:

5146

East Asian (EAS)

AF:

0.244

AC:

920

AN:

3774

South Asian (SAS)

AF:

0.109

AC:

1786

AN:

16456

European-Finnish (FIN)

AF:

0.0931

AC:

AN:

720

Middle Eastern (MID)

AF:

0.140

AC:

227

AN:

1616

European-Non Finnish (NFE)

AF:

0.115

AC:

87237

AN:

761322

Other (OTH)

AF:

0.124

AC:

3386

AN:

27288

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

4401

8802

13202

17603

22004

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0990

AC:

15058

AN:

152028

Hom.:

945

Cov.:

AF XY:

0.0986

AC XY:

7328

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.0269

AC:

1116

AN:

41484

American (AMR)

AF:

0.124

AC:

1897

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

560

AN:

3470

East Asian (EAS)

AF:

0.250

AC:

1292

AN:

5166

South Asian (SAS)

AF:

0.132

AC:

634

AN:

4816

European-Finnish (FIN)

AF:

0.0852

AC:

899

AN:

10548

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8222

AN:

67954

Other (OTH)

AF:

0.127

AC:

269

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

688

1375

2063

2750

3438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.119

Hom.:

1350

Bravo

AF:

0.100

Asia WGS

AF:

0.175

AC:

607

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

4.8

(source)

DANN

Benign

0.81

PhyloP100

-0.35

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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rs16870224

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over