chr7-139991120-A-T

Position:

• chr7-139991120-A-T

Variant summary

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

The NM_001061.7(TBXAS1):​c.1135-15971A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 152,310 control chromosomes in the GnomAD database, including 408 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 0.064 (408 hom., cov: 31)
• Consequence: TBXAS1 NM_001061.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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]

TBXAS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBXAS1	NM_001061.7	c.1135-15971A>T		intron_variant		ENST00000448866.7	NP_001052.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBXAS1	ENST00000448866.7	c.1135-15971A>T		intron_variant		1	NM_001061.7	ENSP00000402536.3

Frequencies

GnomAD3 genomes AF: 0.0637 AC: 9690 AN: 152192 Hom.: 408 Cov.: 31

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0579

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0852

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.0636 AC: 9686 AN: 152310 Hom.: 408 Cov.: 31 AF XY: 0.0634 AC XY: 4723 AN XY: 74470

Gnomad4 AFR AF: 0.0173

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.0672

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0753

Gnomad4 NFE AF: 0.0852

Gnomad4 OTH AF: 0.0838

Alfa AF: 0.0414 Hom.: 33

Bravo AF: 0.0578

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.10
DANN	Benign	0.77

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: rs8192856; hg19: chr7-139690919;