rs634681

Variant names:

• chr11-60854188-G-A
• rs634681
• NM_004778.3:c.-9-457C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PTGDR2	NM_004778.3	c.-9-457C>T		intron_variant	Intron 1 of 1	ENST00000332539.5	NP_004769.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGDR2	ENST00000332539.5	c.-9-457C>T		intron_variant	Intron 1 of 1	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

African (AFR) AF: 0.102 AC: 4224 AN: 41516

American (AMR) AF: 0.289 AC: 4427 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3466

East Asian (EAS) AF: 0.732 AC: 3773 AN: 5154

South Asian (SAS) AF: 0.381 AC: 1837 AN: 4818

European-Finnish (FIN) AF: 0.316 AC: 3338 AN: 10560

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

European-Non Finnish (NFE) AF: 0.236 AC: 16026 AN: 67958

Other (OTH) AF: 0.203 AC: 429 AN: 2114

Alfa AF: 0.237 Hom.: 8410

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
PhyloP100		1.1
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: rs634681; hg19: chr11-60621661;