Variant 14-52274879-G-A 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.995G>A(p.Arg332Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00915 in 1,608,706 control chromosomes in the GnomAD database, including 79 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0064 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0094 ( 76 hom. )

Consequence

PTGDR
NM_000953.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.30

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0035287142).

BP6

Variant 14-52274879-G-A is Benign according to our data. Variant chr14-52274879-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2644239.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PTGDR	NM_000953.3 linkuse as main transcript	c.995G>A	p.Arg332Gln	missense_variant	2/2	ENST00000306051.3
PTGDR	XM_005267891.5 linkuse as main transcript	c.995G>A	p.Arg332Gln	missense_variant	2/3
PTGDR	NM_001281469.2 linkuse as main transcript	c.*195G>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGDR	ENST00000306051.3 linkuse as main transcript	c.995G>A	p.Arg332Gln	missense_variant	2/2	1	NM_000953.3	P1	Q13258-1
PTGDR	ENST00000553372.1 linkuse as main transcript	c.*195G>A		3_prime_UTR_variant	3/3	3			Q13258-2

Frequencies

GnomAD3 genomes

AF:

0.00642

AC:

974

AN:

151824

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00283

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00682

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.000773

Gnomad SAS

AF:

0.00250

Gnomad FIN

AF:

0.00209

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00952

Gnomad OTH

AF:

0.00575

GnomAD3 exomes

AF:

0.00671

AC:

1685

AN:

251206

Hom.:

AF XY:

0.00697

AC XY:

946

AN XY:

135796

show subpopulations

Gnomad AFR exome

AF:

0.00228

Gnomad AMR exome

AF:

0.00619

Gnomad ASJ exome

AF:

0.0165

Gnomad EAS exome

AF:

0.000544

Gnomad SAS exome

AF:

0.00235

Gnomad FIN exome

AF:

0.00148

Gnomad NFE exome

AF:

0.00969

Gnomad OTH exome

AF:

0.00865

GnomAD4 exome

AF:

0.00943

AC:

13744

AN:

1456764

Hom.:

Cov.:

AF XY:

0.00926

AC XY:

6713

AN XY:

724922

show subpopulations

Gnomad4 AFR exome

AF:

0.00180

Gnomad4 AMR exome

AF:

0.00684

Gnomad4 ASJ exome

AF:

0.0152

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.00259

Gnomad4 FIN exome

AF:

0.00245

Gnomad4 NFE exome

AF:

0.0110

Gnomad4 OTH exome

AF:

0.00756

GnomAD4 genome

AF:

0.00641

AC:

974

AN:

151942

Hom.:

Cov.:

AF XY:

0.00553

AC XY:

411

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.00282

Gnomad4 AMR

AF:

0.00681

Gnomad4 ASJ

AF:

0.0150

Gnomad4 EAS

AF:

0.000775

Gnomad4 SAS

AF:

0.00250

Gnomad4 FIN

AF:

0.00209

Gnomad4 NFE

AF:

0.00952

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00942

Hom.:

Bravo

AF:

0.00718

TwinsUK

AF:

0.0111

AC:

ALSPAC

AF:

0.00856

AC:

ESP6500AA

AF:

0.00363

AC:

ESP6500EA

AF:

0.0107

AC:

ExAC

AF:

0.00670

AC:

814

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.0103

EpiControl

AF:

0.0127

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

Jan 01, 2023

PTGDR: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.37

Cadd

Pathogenic

Dann

Pathogenic

1.0

DEOGEN2

Benign

0.24

Eigen

Uncertain

0.33

Eigen_PC

Uncertain

0.41

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.76

MetaRNN

Benign

0.0035

MetaSVM

Benign

-0.94

MutationAssessor

Benign

0.97

MutationTaster

Benign

1.0

D;D

PrimateAI

Benign

0.38

PROVEAN

Benign

-1.1

REVEL

Benign

0.10

Sift

Benign

0.20

Sift4G

Benign

0.14

Polyphen

0.97

Vest4

0.51

MVP

0.70

MPC

1.1

ClinPred

0.026

GERP RS

5.2

Varity_R

0.14

gMVP

0.72

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