7-139879378-C-T

Position:

• chr7-139879378-C-T

Variant summary

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

The NM_001061.7(TBXAS1):​c.236+3741C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0622 in 152,078 control chromosomes in the GnomAD database, including 401 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 0.062 (401 hom., cov: 32)
• Consequence: TBXAS1 NM_001061.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBXAS1	NM_001061.7	c.236+3741C>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.236+3741C>T		intron_variant		1	NM_001061.7	ENSP00000402536	P1

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9440 AN: 151960 Hom.: 394 Cov.: 32

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0497

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0622 AC: 9458 AN: 152078 Hom.: 401 Cov.: 32 AF XY: 0.0653 AC XY: 4851 AN XY: 74328

Gnomad4 AFR AF: 0.0520

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0649

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.0561

Gnomad4 FIN AF: 0.0715

Gnomad4 NFE AF: 0.0497

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0530 Hom.: 353

Bravo AF: 0.0650

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.1
DANN	Benign	0.24

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: rs8192813; hg19: chr7-139579177;