9-136978984-T-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000954.6(PTGDS):c.115-9T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00542 in 1,604,416 control chromosomes in the GnomAD database, including 422 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.029 ( 225 hom., cov: 33)
Exomes 𝑓: 0.0030 ( 197 hom. )
Consequence
PTGDS
NM_000954.6 splice_polypyrimidine_tract, intron
NM_000954.6 splice_polypyrimidine_tract, intron
Scores
1
1
Splicing: ADA: 0.09194
2
Clinical Significance
Conservation
PhyloP100: 0.670
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 9-136978984-T-C is Benign according to our data. Variant chr9-136978984-T-C is described in ClinVar as [Benign]. Clinvar id is 768340.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGDS | NM_000954.6 | c.115-9T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000371625.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGDS | ENST00000371625.8 | c.115-9T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000954.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0288 AC: 4366AN: 151392Hom.: 225 Cov.: 33
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GnomAD3 exomes AF: 0.00740 AC: 1727AN: 233236Hom.: 64 AF XY: 0.00544 AC XY: 696AN XY: 128028
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GnomAD4 exome AF: 0.00297 AC: 4317AN: 1452902Hom.: 197 Cov.: 32 AF XY: 0.00251 AC XY: 1814AN XY: 722786
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GnomAD4 genome AF: 0.0289 AC: 4373AN: 151514Hom.: 225 Cov.: 33 AF XY: 0.0284 AC XY: 2101AN XY: 74030
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at