11-60852184-T-C

Variant names:

• chr11-60852184-T-C
• rs545659
• NM_004778.3:c.*351A>G

Variant summary

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

The NM_004778.3(PTGDR2):​c.*351A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 257,520 control chromosomes in the GnomAD database, including 10,081 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 (5248 hom., cov: 33)
  • Exomes 𝑓: 0.25 (4833 hom.)
• Consequence: PTGDR2 NM_004778.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18
• Publications: 16 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=-1.01).
• 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.*351A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000332539.5	NP_004769.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGDR2	ENST00000332539.5	c.*351A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_004778.3	ENSP00000332812.4

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34801 AN: 152040 Hom.: 5248 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.200

GnomAD4 exome AF: 0.255 AC: 26844 AN: 105362 Hom.: 4833 Cov.: 0 AF XY: 0.253 AC XY: 13389 AN XY: 52858

African (AFR) AF: 0.0906 AC: 346 AN: 3818

American (AMR) AF: 0.299 AC: 865 AN: 2894

Ashkenazi Jewish (ASJ) AF: 0.0670 AC: 295 AN: 4404

East Asian (EAS) AF: 0.694 AC: 6068 AN: 8748

South Asian (SAS) AF: 0.350 AC: 323 AN: 924

European-Finnish (FIN) AF: 0.287 AC: 2270 AN: 7922

Middle Eastern (MID) AF: 0.0675 AC: 44 AN: 652

European-Non Finnish (NFE) AF: 0.218 AC: 14978 AN: 68790

Other (OTH) AF: 0.230 AC: 1655 AN: 7210

GnomAD4 genome AF: 0.229 AC: 34817 AN: 152158 Hom.: 5248 Cov.: 33 AF XY: 0.239 AC XY: 17761 AN XY: 74372

African (AFR) AF: 0.102 AC: 4254 AN: 41554

American (AMR) AF: 0.290 AC: 4434 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0767 AC: 266 AN: 3470

East Asian (EAS) AF: 0.733 AC: 3775 AN: 5152

South Asian (SAS) AF: 0.390 AC: 1877 AN: 4818

European-Finnish (FIN) AF: 0.320 AC: 3389 AN: 10580

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

European-Non Finnish (NFE) AF: 0.238 AC: 16168 AN: 67972

Other (OTH) AF: 0.203 AC: 429 AN: 2110

Alfa AF: 0.126 Hom.: 247

Bravo AF: 0.222

Asia WGS AF: 0.487 AC: 1692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.056
DANN	Benign	0.24
PhyloP100		-3.2
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: rs545659; hg19: chr11-60619657;