rs634681

Positions:

• chr11-60854188-G-A

Variant summary

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

The NM_004778.3(PTGDR2):​c.-9-457C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,084 control chromosomes in the GnomAD database, including 5,168 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 0.23 (5168 hom., cov: 32)
• Consequence: PTGDR2 NM_004778.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGDR2	NM_004778.3	c.-9-457C>T		intron_variant		ENST00000332539.5	NP_004769.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGDR2	ENST00000332539.5	c.-9-457C>T		intron_variant		1	NM_004778.3	ENSP00000332812.4

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34531 AN: 151966 Hom.: 5168 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.227 AC: 34546 AN: 152084 Hom.: 5168 Cov.: 32 AF XY: 0.237 AC XY: 17635 AN XY: 74328

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.203

Alfa AF: 0.228 Hom.: 2133

Bravo AF: 0.221

Asia WGS AF: 0.484 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.0
DANN	Benign	0.72

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: rs634681; hg19: chr11-60621661;