rs1953367

Variant names:

• chr14-52279352-A-G
• rs1953367
• XM_005267891.5:c.*3410A>G

Variant summary

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

The XM_005267891.5(PTGDR):​c.*3410A>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 0.236 in 152,206 control chromosomes in the GnomAD database, including 4,466 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 0.24 (4466 hom., cov: 32)
• Consequence: PTGDR XM_005267891.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGDR	XM_005267891.5	c.*3410A>G		3_prime_UTR_variant	Exon 3 of 3		XP_005267948.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289424	ENST00000726797.1	n.300-9807T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35977 AN: 152088 Hom.: 4458 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.236 AC: 35992 AN: 152206 Hom.: 4466 Cov.: 32 AF XY: 0.235 AC XY: 17498 AN XY: 74412

African (AFR) AF: 0.168 AC: 6979 AN: 41546

American (AMR) AF: 0.278 AC: 4252 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1126 AN: 3468

East Asian (EAS) AF: 0.154 AC: 800 AN: 5180

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4824

European-Finnish (FIN) AF: 0.260 AC: 2757 AN: 10586

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18170 AN: 67994

Other (OTH) AF: 0.257 AC: 544 AN: 2114

Alfa AF: 0.255 Hom.: 2789

Bravo AF: 0.235

Asia WGS AF: 0.202 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.56
PhyloP100		0.094

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1953367; hg19: chr14-52746070;