rs17125273
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000953.3(PTGDR):c.1044G>A(p.Arg348=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 1,595,796 control chromosomes in the GnomAD database, including 11,751 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 0.099 ( 889 hom., cov: 32)
Exomes 𝑓: 0.12 ( 10862 hom. )
Consequence
PTGDR
NM_000953.3 synonymous
NM_000953.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.05
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP7
?
Synonymous conserved (PhyloP=1.05 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGDR | NM_000953.3 | c.1044G>A | p.Arg348= | synonymous_variant | 2/2 | ENST00000306051.3 | |
PTGDR | XM_005267891.5 | c.1044G>A | p.Arg348= | synonymous_variant | 2/3 | ||
PTGDR | NM_001281469.2 | c.*244G>A | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGDR | ENST00000306051.3 | c.1044G>A | p.Arg348= | synonymous_variant | 2/2 | 1 | NM_000953.3 | P1 | |
PTGDR | ENST00000553372.1 | c.*244G>A | 3_prime_UTR_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0994 AC: 15077AN: 151738Hom.: 886 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
15077
AN:
151738
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.111 AC: 27457AN: 248436Hom.: 1873 AF XY: 0.120 AC XY: 16080AN XY: 134200
GnomAD3 exomes
AF:
AC:
27457
AN:
248436
Hom.:
AF XY:
AC XY:
16080
AN XY:
134200
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.118 AC: 169788AN: 1443940Hom.: 10862 Cov.: 32 AF XY: 0.121 AC XY: 87144AN XY: 719170
GnomAD4 exome
AF:
AC:
169788
AN:
1443940
Hom.:
Cov.:
32
AF XY:
AC XY:
87144
AN XY:
719170
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0993 AC: 15086AN: 151856Hom.: 889 Cov.: 32 AF XY: 0.0999 AC XY: 7409AN XY: 74186
GnomAD4 genome
?
AF:
AC:
15086
AN:
151856
Hom.:
Cov.:
32
AF XY:
AC XY:
7409
AN XY:
74186
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
260
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at