rs4726473

Variant summary

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

The NM_001061.7(TBXAS1):​c.450+4790T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,126 control chromosomes in the GnomAD database, including 44,163 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 0.76 ( 44163 hom., cov: 32)

Consequence

TBXAS1
NM_001061.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.15
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TBXAS1NM_001061.7 linkuse as main transcriptc.450+4790T>C intron_variant ENST00000448866.7 NP_001052.3
LOC105375532XR_928043.3 linkuse as main transcriptn.4785T>C non_coding_transcript_exon_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TBXAS1ENST00000448866.7 linkuse as main transcriptc.450+4790T>C intron_variant 1 NM_001061.7 ENSP00000402536 P1P24557-1

Frequencies

GnomAD3 genomes
AF:
0.762
AC:
115756
AN:
152008
Hom.:
44134
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.780
Gnomad AMI
AF:
0.738
Gnomad AMR
AF:
0.798
Gnomad ASJ
AF:
0.741
Gnomad EAS
AF:
0.737
Gnomad SAS
AF:
0.739
Gnomad FIN
AF:
0.687
Gnomad MID
AF:
0.791
Gnomad NFE
AF:
0.758
Gnomad OTH
AF:
0.765
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.761
AC:
115840
AN:
152126
Hom.:
44163
Cov.:
32
AF XY:
0.758
AC XY:
56377
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.780
Gnomad4 AMR
AF:
0.799
Gnomad4 ASJ
AF:
0.741
Gnomad4 EAS
AF:
0.737
Gnomad4 SAS
AF:
0.738
Gnomad4 FIN
AF:
0.687
Gnomad4 NFE
AF:
0.758
Gnomad4 OTH
AF:
0.762
Alfa
AF:
0.758
Hom.:
57296
Bravo
AF:
0.771
Asia WGS
AF:
0.751
AC:
2612
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.95
DANN
Benign
0.64

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: rs4726473; hg19: chr7-139640896; API