Genetic Variant TBXA2R:p.Ser145Ser (chr19-3600200-C-T) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001060.6(TBXA2R):c.435G>A(p.Ser145Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0605 in 1,598,096 control chromosomes in the GnomAD database, including 3,275 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.046 ( 210 hom., cov: 32)

Exomes 𝑓: 0.062 ( 3065 hom. )

Consequence

TBXA2R
NM_001060.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.837

Variant links:

Genes affected

TBXA2R (HGNC:11608): (thromboxane A2 receptor) This gene encodes a member of the G protein-coupled receptor family. The protein interacts with thromboxane A2 to induce platelet aggregation and regulate hemostasis. A mutation in this gene results in a bleeding disorder. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]

TBXA2R links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 19-3600200-C-T is Benign according to our data. Variant chr19-3600200-C-T is described in ClinVar as [Benign]. Clinvar id is 263267.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.837 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6 link	c.435G>A	p.Ser145Ser	synonymous_variant	Exon 2 of 3	ENST00000375190.10	NP_001051.1	P21731-3Q05C92Q0VAB0
TBXA2R	NM_201636.3 link	c.435G>A	p.Ser145Ser	synonymous_variant	Exon 2 of 4		NP_963998.2	P21731-2Q05C92Q0VAB0
TBXA2R	XM_011528214.3 link	c.435G>A	p.Ser145Ser	synonymous_variant	Exon 3 of 4		XP_011526516.1	P21731-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TBXA2R	ENST00000375190.10 link	c.435G>A	p.Ser145Ser	synonymous_variant	Exon 2 of 3	1	NM_001060.6	ENSP00000364336.4	P21731-3
TBXA2R	ENST00000589966.1 link	c.397+38G>A		intron_variant	Intron 1 of 1	1		ENSP00000468145.1	K7ER80
TBXA2R	ENST00000411851.3 link	c.435G>A	p.Ser145Ser	synonymous_variant	Exon 2 of 4	2		ENSP00000393333.2	P21731-2
TBXA2R	ENST00000587717.1 link	n.-67G>A		upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0465

AC:

7069

AN:

151962

Hom.:

210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0110

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0438

Gnomad ASJ

AF:

0.0905

Gnomad EAS

AF:

0.0644

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.0373

Gnomad MID

AF:

0.0732

Gnomad NFE

AF:

0.0627

Gnomad OTH

AF:

0.0479

GnomAD3 exomes

AF:

0.0622

AC:

13129

AN:

210950

Hom.:

509

AF XY:

0.0667

AC XY:

7811

AN XY:

117150

show subpopulations

Gnomad AFR exome

AF:

0.00996

Gnomad AMR exome

AF:

0.0266

Gnomad ASJ exome

AF:

0.0827

Gnomad EAS exome

AF:

0.0746

Gnomad SAS exome

AF:

0.114

Gnomad FIN exome

AF:

0.0398

Gnomad NFE exome

AF:

0.0650

Gnomad OTH exome

AF:

0.0610

GnomAD4 exome

AF:

0.0620

AC:

89656

AN:

1446018

Hom.:

3065

Cov.:

AF XY:

0.0639

AC XY:

45908

AN XY:

718398

show subpopulations

Gnomad4 AFR exome

AF:

0.00938

Gnomad4 AMR exome

AF:

0.0278

Gnomad4 ASJ exome

AF:

0.0820

Gnomad4 EAS exome

AF:

0.0592

Gnomad4 SAS exome

AF:

0.110

Gnomad4 FIN exome

AF:

0.0400

Gnomad4 NFE exome

AF:

0.0617

Gnomad4 OTH exome

AF:

0.0634

GnomAD4 genome

AF:

0.0465

AC:

7071

AN:

152078

Hom.:

210

Cov.:

AF XY:

0.0465

AC XY:

3456

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.0109

Gnomad4 AMR

AF:

0.0438

Gnomad4 ASJ

AF:

0.0905

Gnomad4 EAS

AF:

0.0642

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.0373

Gnomad4 NFE

AF:

0.0628

Gnomad4 OTH

AF:

0.0484

Alfa

AF:

0.0410

Hom.:

Bravo

AF:

0.0446

Asia WGS

AF:

0.0740

AC:

257

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

0.46

DANN

Benign

0.96

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over