rs2072190

chr7-140019384-G-Achr7-140019384-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001061.7(TBXAS1):c.1528-641G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,978 control chromosomes in the GnomAD database, including 24,010 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 0.53 (24010 hom., cov: 31)
• Consequence: TBXAS1 NM_001061.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBXAS1	NM_001061.7	c.1528-641G>A		intron_variant		ENST00000448866.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBXAS1	ENST00000448866.7	c.1528-641G>A		intron_variant		1	NM_001061.7	P1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80223 AN: 151860 Hom.: 23954 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.538

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.529 AC: 80336 AN: 151978 Hom.: 24010 Cov.: 31 AF XY: 0.524 AC XY: 38897 AN XY: 74290

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.536

Alfa AF: 0.418 Hom.: 18546

Bravo AF: 0.564

Asia WGS AF: 0.459 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.43
Dann	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2072190; hg19: chr7-139719184;