14-52273723-C-G

Variant names:

• chr14-52273723-C-G
• rs10498445
• NM_000953.3:c.847-1008C>G

Variant summary

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

The NM_000953.3(PTGDR):​c.847-1008C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,182 control chromosomes in the GnomAD database, including 3,563 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 0.19 (3563 hom., cov: 32)
• Consequence: PTGDR NM_000953.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101
• Publications: 5 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGDR	NM_000953.3	c.847-1008C>G		intron_variant	Intron 1 of 1	ENST00000306051.3	NP_000944.1
PTGDR	NM_001281469.2	c.*47-1008C>G		intron_variant	Intron 2 of 2		NP_001268398.1
PTGDR	XM_005267891.5	c.847-1008C>G		intron_variant	Intron 1 of 2		XP_005267948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGDR	ENST00000306051.3	c.847-1008C>G		intron_variant	Intron 1 of 1	1	NM_000953.3	ENSP00000303424.2
PTGDR	ENST00000553372.1	c.*47-1008C>G		intron_variant	Intron 2 of 2	3		ENSP00000452408.1
ENSG00000289424	ENST00000726797.1	n.300-4178G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29685 AN: 152064 Hom.: 3567 Cov.: 32

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.228

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.195 AC: 29669 AN: 152182 Hom.: 3563 Cov.: 32 AF XY: 0.192 AC XY: 14311 AN XY: 74394

African (AFR) AF: 0.0667 AC: 2771 AN: 41556

American (AMR) AF: 0.168 AC: 2563 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1125 AN: 3470

East Asian (EAS) AF: 0.109 AC: 565 AN: 5174

South Asian (SAS) AF: 0.209 AC: 1005 AN: 4818

European-Finnish (FIN) AF: 0.260 AC: 2742 AN: 10566

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18097 AN: 67994

Other (OTH) AF: 0.225 AC: 475 AN: 2110

Alfa AF: 0.134 Hom.: 279

Bravo AF: 0.182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.1
DANN	Benign	0.52
PhyloP100		-0.10
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: rs10498445; hg19: chr14-52740441;