Variant chr19-3595796-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000589966.1(TBXA2R):c.535T>C(p.Tyr179His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 1,610,200 control chromosomes in the GnomAD database, including 324,213 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.65 ( 33368 hom., cov: 33)

Exomes 𝑓: 0.62 ( 290845 hom. )

Consequence

TBXA2R
ENST00000589966.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.82

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.0298587E-6).

BP6

Variant 19-3595796-A-G is Benign according to our data. Variant chr19-3595796-A-G is described in ClinVar as [Benign]. Clinvar id is 263269.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TBXA2R	NM_001060.6 linkuse as main transcript	c.924T>C	p.Tyr308=	synonymous_variant	3/3	ENST00000375190.10
TBXA2R	NM_201636.3 linkuse as main transcript	c.924T>C	p.Tyr308=	synonymous_variant	3/4
TBXA2R	XM_011528214.3 linkuse as main transcript	c.924T>C	p.Tyr308=	synonymous_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBXA2R	ENST00000589966.1 linkuse as main transcript	c.535T>C	p.Tyr179His	missense_variant	2/2	1
TBXA2R	ENST00000375190.10 linkuse as main transcript	c.924T>C	p.Tyr308=	synonymous_variant	3/3	1	NM_001060.6	P1	P21731-3
TBXA2R	ENST00000411851.3 linkuse as main transcript	c.924T>C	p.Tyr308=	synonymous_variant	3/4	2			P21731-2

Frequencies

GnomAD3 genomes

AF:

0.649

AC:

98634

AN:

151994

Hom.:

33324

Cov.:

show subpopulations

Gnomad AFR

AF:

0.777

Gnomad AMI

AF:

0.460

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.625

Gnomad EAS

AF:

0.180

Gnomad SAS

AF:

0.462

Gnomad FIN

AF:

0.627

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.652

Gnomad OTH

AF:

0.655

GnomAD3 exomes

AF:

0.564

AC:

135033

AN:

239524

Hom.:

41042

AF XY:

0.568

AC XY:

74212

AN XY:

130666

show subpopulations

Gnomad AFR exome

AF:

0.787

Gnomad AMR exome

AF:

0.381

Gnomad ASJ exome

AF:

0.621

Gnomad EAS exome

AF:

0.188

Gnomad SAS exome

AF:

0.484

Gnomad FIN exome

AF:

0.629

Gnomad NFE exome

AF:

0.654

Gnomad OTH exome

AF:

0.605

GnomAD4 exome

AF:

0.623

AC:

908536

AN:

1458088

Hom.:

290845

Cov.:

103

AF XY:

0.620

AC XY:

449455

AN XY:

725094

show subpopulations

Gnomad4 AFR exome

AF:

0.789

Gnomad4 AMR exome

AF:

0.402

Gnomad4 ASJ exome

AF:

0.617

Gnomad4 EAS exome

AF:

0.174

Gnomad4 SAS exome

AF:

0.481

Gnomad4 FIN exome

AF:

0.627

Gnomad4 NFE exome

AF:

0.655

Gnomad4 OTH exome

AF:

0.606

GnomAD4 genome

AF:

0.649

AC:

98729

AN:

152112

Hom.:

33368

Cov.:

AF XY:

0.642

AC XY:

47749

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.778

Gnomad4 AMR

AF:

0.535

Gnomad4 ASJ

AF:

0.625

Gnomad4 EAS

AF:

0.180

Gnomad4 SAS

AF:

0.462

Gnomad4 FIN

AF:

0.627

Gnomad4 NFE

AF:

0.652

Gnomad4 OTH

AF:

0.652

Alfa

AF:

0.661

Hom.:

17771

Bravo

AF:

0.646

TwinsUK

AF:

0.653

AC:

2423

ALSPAC

AF:

0.653

AC:

2515

ESP6500AA

AF:

0.798

AC:

3482

ESP6500EA

AF:

0.655

AC:

5600

ExAC

AF:

0.569

AC:

68510

Asia WGS

AF:

0.395

AC:

1377

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	This variant is associated with the following publications: (PMID: 28709878, 10830912) -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.32

CADD

Benign

9.4

DANN

Benign

0.80

FATHMM_MKL

Benign

0.045

LIST_S2

Benign

0.20

MetaRNN

Benign

0.0000010

MutationTaster

Benign

0.96

P;P;P

Sift4G

Benign

0.20

Vest4

0.22

GERP RS

3.1

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