rs11571288

chr11-60852291-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004778.3(PTGDR2):c.*244G>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 0.302 in 393,464 control chromosomes in the GnomAD database, including 18,314 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 0.30 (6838 hom., cov: 33)
  • Exomes 𝑓: 0.31 (11476 hom.)
• Consequence: PTGDR2 NM_004778.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

Genes affected

PTGDR2 (HGNC:4502): (prostaglandin D2 receptor 2) This gene encodes a G-protein-coupled receptor that is preferentially expressed in CD4+ effector T helper 2 (Th2) cells. This protein is a prostaglandin D2 receptor that mediates the pro-inflammatory chemotaxis of eosinophils, basophils, and Th2 lymphocytes generated during allergic inflammation. Single nucleotide polymorphisms in the 3' UTR of this gene have been associated with asthma susceptibility.[provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGDR2	NM_004778.3	c.*244G>C		3_prime_UTR_variant	2/2	ENST00000332539.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGDR2	ENST00000332539.5	c.*244G>C		3_prime_UTR_variant	2/2	1	NM_004778.3	P1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45063 AN: 152074 Hom.: 6837 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.291

GnomAD4 exome AF: 0.305 AC: 73702 AN: 241270 Hom.: 11476 Cov.: 4 AF XY: 0.306 AC XY: 37358 AN XY: 122254

Gnomad4 AFR exome AF: 0.257

Gnomad4 AMR exome AF: 0.346

Gnomad4 ASJ exome AF: 0.387

Gnomad4 EAS exome AF: 0.212

Gnomad4 SAS exome AF: 0.272

Gnomad4 FIN exome AF: 0.290

Gnomad4 NFE exome AF: 0.317

Gnomad4 OTH exome AF: 0.299

GnomAD4 genome AF: 0.296 AC: 45084 AN: 152194 Hom.: 6838 Cov.: 33 AF XY: 0.296 AC XY: 22009 AN XY: 74394

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.289

Alfa AF: 0.301 Hom.: 865

Bravo AF: 0.297

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.7
Dann	Benign	0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs11571288; hg19: chr11-60619764;