chr9-136980066-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000954.6(PTGDS):c.448+4C>T variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000553 in 1,610,182 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0032 ( 3 hom., cov: 33)
Exomes 𝑓: 0.00028 ( 2 hom. )
Consequence
PTGDS
NM_000954.6 splice_donor_region, intron
NM_000954.6 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0004218
2
Clinical Significance
Conservation
PhyloP100: -0.958
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 9-136980066-C-T is Benign according to our data. Variant chr9-136980066-C-T is described in ClinVar as [Benign]. Clinvar id is 785302.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGDS | NM_000954.6 | c.448+4C>T | splice_donor_region_variant, intron_variant | ENST00000371625.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGDS | ENST00000371625.8 | c.448+4C>T | splice_donor_region_variant, intron_variant | 1 | NM_000954.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00316 AC: 480AN: 152114Hom.: 3 Cov.: 33
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GnomAD3 exomes AF: 0.000784 AC: 194AN: 247460Hom.: 2 AF XY: 0.000568 AC XY: 76AN XY: 133868
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GnomAD4 exome AF: 0.000281 AC: 409AN: 1457950Hom.: 2 Cov.: 31 AF XY: 0.000226 AC XY: 164AN XY: 725258
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GnomAD4 genome AF: 0.00316 AC: 481AN: 152232Hom.: 3 Cov.: 33 AF XY: 0.00305 AC XY: 227AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 03, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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