chr7-139828863-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000336425.10(TBXAS1):c.-79-449G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,128 control chromosomes in the GnomAD database, including 37,347 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.68 ( 37347 hom., cov: 32)
Consequence
TBXAS1
ENST00000336425.10 intron
ENST00000336425.10 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.427
Genes affected
TBXAS1 (HGNC:11609): (thromboxane A synthase 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. However, this protein is considered a member of the cytochrome P450 superfamily on the basis of sequence similarity rather than functional similarity. This endoplasmic reticulum membrane protein catalyzes the conversion of prostglandin H2 to thromboxane A2, a potent vasoconstrictor and inducer of platelet aggregation. The enzyme plays a role in several pathophysiological processes including hemostasis, cardiovascular disease, and stroke. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 7-139828863-G-T is Benign according to our data. Variant chr7-139828863-G-T is described in ClinVar as [Benign]. Clinvar id is 1227899.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBXAS1 | NM_001130966.5 | c.-79-449G>T | intron_variant | ||||
TBXAS1 | NM_001166254.4 | c.-113+41437G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBXAS1 | ENST00000336425.10 | c.-79-449G>T | intron_variant | 1 | P1 | ||||
TBXAS1 | ENST00000425687.5 | c.-113+41437G>T | intron_variant | 1 | |||||
TBXAS1 | ENST00000438104.6 | c.-79-449G>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.682 AC: 103733AN: 152010Hom.: 37282 Cov.: 32
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GnomAD4 genome ? AF: 0.683 AC: 103859AN: 152128Hom.: 37347 Cov.: 32 AF XY: 0.685 AC XY: 50958AN XY: 74358
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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 | GeneDx | Nov 12, 2018 | - - |
Computational scores
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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