Variant chr14-52268572-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_000953.3(PTGDR):c.758C>G(p.Ala253Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00448 in 1,612,484 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 2 hom., cov: 33)

Exomes 𝑓: 0.0046 ( 20 hom. )

Consequence

PTGDR
NM_000953.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.62

Variant links:

Genes affected

PTGDR (HGNC:9591): (prostaglandin D2 receptor) This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor (GPCR) superfamily. The receptors are seven-pass transmembrane proteins that respond to extracellular cues and activate intracellular signal transduction pathways. This protein is reported to be a receptor for prostaglandin D2, which is a mediator of allergic inflammation and allergic airway inflammation in asthma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

PTGDR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004047811).

BP6

Variant 14-52268572-C-G is Benign according to our data. Variant chr14-52268572-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 3250544.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGDR	NM_000953.3 linkuse as main transcript	c.758C>G	p.Ala253Gly	missense_variant	1/2	ENST00000306051.3	NP_000944.1	Q13258-1
PTGDR	NM_001281469.2 linkuse as main transcript	c.758C>G	p.Ala253Gly	missense_variant	1/3		NP_001268398.1	Q13258-2
PTGDR	XM_005267891.5 linkuse as main transcript	c.758C>G	p.Ala253Gly	missense_variant	1/3		XP_005267948.1	Q13258-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGDR	ENST00000306051.3 linkuse as main transcript	c.758C>G	p.Ala253Gly	missense_variant	1/2	1	NM_000953.3	ENSP00000303424.2		Q13258-1
PTGDR	ENST00000553372.1 linkuse as main transcript	c.758C>G	p.Ala253Gly	missense_variant	1/3	3		ENSP00000452408.1		Q13258-2

Frequencies

GnomAD3 genomes

AF:

0.00326

AC:

496

AN:

152218

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00125

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00536

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000829

Gnomad FIN

AF:

0.00141

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00497

Gnomad OTH

AF:

0.00191

GnomAD3 exomes

AF:

0.00277

AC:

682

AN:

245854

Hom.:

AF XY:

0.00272

AC XY:

363

AN XY:

133594

show subpopulations

Gnomad AFR exome

AF:

0.00134

Gnomad AMR exome

AF:

0.00287

Gnomad ASJ exome

AF:

0.000101

Gnomad EAS exome

AF:

0.0000546

Gnomad SAS exome

AF:

0.000656

Gnomad FIN exome

AF:

0.00233

Gnomad NFE exome

AF:

0.00429

Gnomad OTH exome

AF:

0.00331

GnomAD4 exome

AF:

0.00460

AC:

6723

AN:

1460148

Hom.:

Cov.:

AF XY:

0.00442

AC XY:

3208

AN XY:

726348

show subpopulations

Gnomad4 AFR exome

AF:

0.00108

Gnomad4 AMR exome

AF:

0.00329

Gnomad4 ASJ exome

AF:

0.0000767

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000604

Gnomad4 FIN exome

AF:

0.00253

Gnomad4 NFE exome

AF:

0.00545

Gnomad4 OTH exome

AF:

0.00472

GnomAD4 genome

AF:

0.00326

AC:

496

AN:

152336

Hom.:

Cov.:

AF XY:

0.00315

AC XY:

235

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.00125

Gnomad4 AMR

AF:

0.00536

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000830

Gnomad4 FIN

AF:

0.00141

Gnomad4 NFE

AF:

0.00497

Gnomad4 OTH

AF:

0.00189

Alfa

AF:

0.00381

Hom.:

Bravo

AF:

0.00353

TwinsUK

AF:

0.00566

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.00114

AC:

ESP6500EA

AF:

0.00442

AC:

ExAC

AF:

0.00289

AC:

350

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jun 01, 2024

PTGDR: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.55

CADD

Benign

0.79

DANN

Benign

0.75

DEOGEN2

Benign

0.061

T;.

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.14

LIST_S2

Benign

0.56

T;T

M_CAP

Benign

0.0033

MetaRNN

Benign

0.0040

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.0

L;L

PrimateAI

Benign

0.43

PROVEAN

Benign

0.58

N;N

REVEL

Benign

0.076

Sift

Benign

0.43

T;T

Sift4G

Benign

0.42

T;T

Polyphen

0.0010

B;.

Vest4

0.15

MVP

0.28

MPC

0.33

ClinPred

0.0049

GERP RS

-1.6

Varity_R

0.039

gMVP

0.12

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

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