Variant rs4880179 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000954.6(PTGDS):c.18A>G(p.Thr6Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.963 in 1,601,766 control chromosomes in the GnomAD database, including 743,442 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 0.95 ( 68606 hom., cov: 35)

Exomes 𝑓: 0.96 ( 674836 hom. )

Consequence

PTGDS
NM_000954.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.73

Variant links:

Genes affected

PTGDS (HGNC:9592): (prostaglandin D2 synthase) The protein encoded by this gene is a glutathione-independent prostaglandin D synthase that catalyzes the conversion of prostaglandin H2 (PGH2) to postaglandin D2 (PGD2). PGD2 functions as a neuromodulator as well as a trophic factor in the central nervous system. PGD2 is also involved in smooth muscle contraction/relaxation and is a potent inhibitor of platelet aggregation. This gene is preferentially expressed in brain. Studies with transgenic mice overexpressing this gene suggest that this gene may be also involved in the regulation of non-rapid eye movement sleep. [provided by RefSeq, Jul 2008]

PTGDS links:

ENSG00000284341 (HGNC:):

ENSG00000284341 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP7

Synonymous conserved (PhyloP=-2.73 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGDS	NM_000954.6 link	c.18A>G	p.Thr6Thr	synonymous_variant	1/7	ENST00000371625.8	NP_000945.3	P41222A0A024R8G3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGDS	ENST00000371625.8 link	c.18A>G	p.Thr6Thr	synonymous_variant	1/7	1	NM_000954.6	ENSP00000360687.3		P41222
ENSG00000284341	ENST00000471521.5 link	n.18A>G		non_coding_transcript_exon_variant	1/10	5		ENSP00000435033.1

Frequencies

GnomAD3 genomes

AF:

0.949

AC:

144402

AN:

152226

Hom.:

68560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.900

Gnomad AMI

AF:

0.986

Gnomad AMR

AF:

0.966

Gnomad ASJ

AF:

0.960

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.986

Gnomad FIN

AF:

0.966

Gnomad MID

AF:

0.975

Gnomad NFE

AF:

0.964

Gnomad OTH

AF:

0.953

GnomAD3 exomes

AF:

0.968

AC:

228790

AN:

236238

Hom.:

110846

AF XY:

0.970

AC XY:

125455

AN XY:

129324

show subpopulations

Gnomad AFR exome

AF:

0.896

Gnomad AMR exome

AF:

0.981

Gnomad ASJ exome

AF:

0.966

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.984

Gnomad FIN exome

AF:

0.970

Gnomad NFE exome

AF:

0.966

Gnomad OTH exome

AF:

0.966

GnomAD4 exome

AF:

0.965

AC:

1398485

AN:

1449422

Hom.:

674836

Cov.:

AF XY:

0.965

AC XY:

696045

AN XY:

720954

show subpopulations

Gnomad4 AFR exome

AF:

0.896

Gnomad4 AMR exome

AF:

0.979

Gnomad4 ASJ exome

AF:

0.964

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.984

Gnomad4 FIN exome

AF:

0.971

Gnomad4 NFE exome

AF:

0.963

Gnomad4 OTH exome

AF:

0.965

GnomAD4 genome

AF:

0.949

AC:

144507

AN:

152344

Hom.:

68606

Cov.:

AF XY:

0.951

AC XY:

70822

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.900

Gnomad4 AMR

AF:

0.966

Gnomad4 ASJ

AF:

0.960

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.986

Gnomad4 FIN

AF:

0.966

Gnomad4 NFE

AF:

0.964

Gnomad4 OTH

AF:

0.953

Alfa

AF:

0.959

Hom.:

55506

Bravo

AF:

0.947

Asia WGS

AF:

0.989

AC:

3437

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.79

DANN

Benign

0.59

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over