chr7-139984244-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001061.7(TBXAS1):​c.1134+22011T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,938 control chromosomes in the GnomAD database, including 5,459 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 0.26 ( 5459 hom., cov: 32)

Consequence

TBXAS1
NM_001061.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.398
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TBXAS1NM_001061.7 linkc.1134+22011T>G intron_variant Intron 9 of 12 ENST00000448866.7 NP_001052.3 P24557-1Q53F23

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TBXAS1ENST00000448866.7 linkc.1134+22011T>G intron_variant Intron 9 of 12 1 NM_001061.7 ENSP00000402536.3 P24557-1

Frequencies

GnomAD3 genomes
AF:
0.264
AC:
40053
AN:
151820
Hom.:
5459
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.215
Gnomad AMI
AF:
0.390
Gnomad AMR
AF:
0.309
Gnomad ASJ
AF:
0.354
Gnomad EAS
AF:
0.316
Gnomad SAS
AF:
0.415
Gnomad FIN
AF:
0.242
Gnomad MID
AF:
0.386
Gnomad NFE
AF:
0.264
Gnomad OTH
AF:
0.289
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.264
AC:
40054
AN:
151938
Hom.:
5459
Cov.:
32
AF XY:
0.268
AC XY:
19884
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.214
Gnomad4 AMR
AF:
0.310
Gnomad4 ASJ
AF:
0.354
Gnomad4 EAS
AF:
0.316
Gnomad4 SAS
AF:
0.413
Gnomad4 FIN
AF:
0.242
Gnomad4 NFE
AF:
0.265
Gnomad4 OTH
AF:
0.287
Alfa
AF:
0.266
Hom.:
7917
Bravo
AF:
0.263
Asia WGS
AF:
0.321
AC:
1117
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
1.2
DANN
Benign
0.59

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10487667; hg19: chr7-139684043; API