rs4880179
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_000954.6(PTGDS):āc.18A>Gā(p.Thr6=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.963 in 1,601,766 control chromosomes in the GnomAD database, including 743,442 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: š 0.95 ( 68606 hom., cov: 35)
Exomes š: 0.96 ( 674836 hom. )
Consequence
PTGDS
NM_000954.6 synonymous
NM_000954.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.73
Genes affected
PTGDS (HGNC:9592): (prostaglandin D2 synthase) The protein encoded by this gene is a glutathione-independent prostaglandin D synthase that catalyzes the conversion of prostaglandin H2 (PGH2) to postaglandin D2 (PGD2). PGD2 functions as a neuromodulator as well as a trophic factor in the central nervous system. PGD2 is also involved in smooth muscle contraction/relaxation and is a potent inhibitor of platelet aggregation. This gene is preferentially expressed in brain. Studies with transgenic mice overexpressing this gene suggest that this gene may be also involved in the regulation of non-rapid eye movement sleep. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP7
?
Synonymous conserved (PhyloP=-2.73 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGDS | NM_000954.6 | c.18A>G | p.Thr6= | synonymous_variant | 1/7 | ENST00000371625.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGDS | ENST00000371625.8 | c.18A>G | p.Thr6= | synonymous_variant | 1/7 | 1 | NM_000954.6 | P1 | |
PTGDS | ENST00000457950.5 | c.18A>G | p.Thr6= | synonymous_variant | 1/5 | 3 | |||
PTGDS | ENST00000640716.1 | c.18A>G | p.Thr6= | synonymous_variant | 4/5 | 5 | |||
PTGDS | ENST00000371623.5 | n.81A>G | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.949 AC: 144402AN: 152226Hom.: 68560 Cov.: 35
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GnomAD3 exomes AF: 0.968 AC: 228790AN: 236238Hom.: 110846 AF XY: 0.970 AC XY: 125455AN XY: 129324
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GnomAD4 exome AF: 0.965 AC: 1398485AN: 1449422Hom.: 674836 Cov.: 43 AF XY: 0.965 AC XY: 696045AN XY: 720954
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GnomAD4 genome ? AF: 0.949 AC: 144507AN: 152344Hom.: 68606 Cov.: 35 AF XY: 0.951 AC XY: 70822AN XY: 74504
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at