dbSNP rs6926: PTGDS:c.*111A>C (chr9-136981689-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_000954.6(PTGDS):c.*111A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,222 control chromosomes in the GnomAD database, including 39,366 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 0.72 ( 39300 hom., cov: 32)

Exomes 𝑓: 0.74 ( 66 hom. )

Consequence

PTGDS
NM_000954.6 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.235

Publications

13 publications found

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:

LCNL1 (HGNC:34436): (lipocalin like 1) Predicted to enable small molecule binding activity. [provided by Alliance of Genome Resources, Apr 2022]

LCNL1 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGDS	NM_000954.6 link	c.*111A>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000371625.8	NP_000945.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGDS	ENST00000371625.8 link	c.*111A>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_000954.6	ENSP00000360687.3
ENSG00000284341	ENST00000471521.5 link	n.573+834A>C		intron_variant	Intron 6 of 9	5		ENSP00000435033.1

Frequencies

GnomAD3 genomes

AF:

0.718

AC:

109105

AN:

151872

Hom.:

39269

Cov.:

show subpopulations

Gnomad AFR

AF:

0.758

Gnomad AMI

AF:

0.729

Gnomad AMR

AF:

0.645

Gnomad ASJ

AF:

0.719

Gnomad EAS

AF:

0.829

Gnomad SAS

AF:

0.786

Gnomad FIN

AF:

0.658

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.707

Gnomad OTH

AF:

0.727

GnomAD4 exome

AF:

0.735

AC:

172

AN:

234

Hom.:

Cov.:

AF XY:

0.753

AC XY:

125

AN XY:

166

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AF:

0.750

AC:

AN:

European-Non Finnish (NFE)

AF:

0.732

AC:

139

AN:

190

Other (OTH)

AF:

0.778

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.718

AC:

109188

AN:

151988

Hom.:

39300

Cov.:

AF XY:

0.716

AC XY:

53206

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.758

AC:

31433

AN:

41452

American (AMR)

AF:

0.644

AC:

9844

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.719

AC:

2497

AN:

3472

East Asian (EAS)

AF:

0.829

AC:

4279

AN:

5164

South Asian (SAS)

AF:

0.785

AC:

3781

AN:

4814

European-Finnish (FIN)

AF:

0.658

AC:

6950

AN:

10568

Middle Eastern (MID)

AF:

0.687

AC:

202

AN:

294

European-Non Finnish (NFE)

AF:

0.707

AC:

48000

AN:

67930

Other (OTH)

AF:

0.731

AC:

1537

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1643

3285

4928

6570

8213

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

842

1684

2526

3368

4210

<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:

0.716

Hom.:

54338

Bravo

AF:

0.719

Asia WGS

AF:

0.782

AC:

2718

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.8

(source)

DANN

Benign

0.50

PhyloP100

-0.23

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over