NM_000953.3:c.*469G>A

Variant names:

• chr14-52275433-G-A
• rs17831675
• NM_000953.3:c.*469G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000953.3(PTGDR):​c.*469G>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 0.0695 in 156,930 control chromosomes in the GnomAD database, including 505 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 0.069 (488 hom., cov: 32)
  • Exomes 𝑓: 0.082 (17 hom.)
• Consequence: PTGDR NM_000953.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 8 publications found

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]

ENSG00000289424 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000953.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGDR	NM_000953.3	MANE Select	c.*469G>A		3_prime_UTR	Exon 2 of 2	NP_000944.1
	PTGDR	NM_001281469.2		c.*749G>A		3_prime_UTR	Exon 3 of 3	NP_001268398.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGDR	ENST00000306051.3	TSL:1 MANE Select	c.*469G>A		3_prime_UTR	Exon 2 of 2	ENSP00000303424.2
	ENSG00000289424	ENST00000726797.1		n.300-5888C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10496 AN: 151980 Hom.: 486 Cov.: 32

Gnomad AFR AF: 0.0250

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0676

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0865

Gnomad OTH AF: 0.0604

GnomAD4 exome AF: 0.0822 AC: 397 AN: 4832 Hom.: 17 Cov.: 0 AF XY: 0.0855 AC XY: 239 AN XY: 2796

African (AFR) AF: 0.00 AC: 0 AN: 18

American (AMR) AF: 0.0565 AC: 45 AN: 796

Ashkenazi Jewish (ASJ) AF: 0.0417 AC: 1 AN: 24

East Asian (EAS) AF: 0.0769 AC: 14 AN: 182

South Asian (SAS) AF: 0.145 AC: 67 AN: 462

European-Finnish (FIN) AF: 0.0517 AC: 3 AN: 58

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0803 AC: 252 AN: 3138

Other (OTH) AF: 0.0987 AC: 15 AN: 152

GnomAD4 genome AF: 0.0691 AC: 10503 AN: 152098 Hom.: 488 Cov.: 32 AF XY: 0.0701 AC XY: 5213 AN XY: 74328

African (AFR) AF: 0.0250 AC: 1037 AN: 41494

American (AMR) AF: 0.0603 AC: 921 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3470

East Asian (EAS) AF: 0.127 AC: 659 AN: 5174

South Asian (SAS) AF: 0.156 AC: 753 AN: 4814

European-Finnish (FIN) AF: 0.0676 AC: 714 AN: 10558

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0865 AC: 5880 AN: 67996

Other (OTH) AF: 0.0607 AC: 128 AN: 2108

Alfa AF: 0.0738 Hom.: 208

Bravo AF: 0.0660

Asia WGS AF: 0.127 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.30
PhyloP100		0.040
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17831675; hg19: chr14-52742151;