Variant chr19-3595008-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 NM_201636.3(TBXA2R):c.1052T>C(p.Leu351Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,420,466 control chromosomes in the GnomAD database, including 7,354 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 910 hom., cov: 32)

Exomes 𝑓: 0.10 ( 6444 hom. )

Consequence

TBXA2R
NM_201636.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.320

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=0.0019531548).

BP6

Variant 19-3595008-A-G is Benign according to our data. Variant chr19-3595008-A-G is described in ClinVar as [Benign]. Clinvar id is 263265.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBXA2R	NM_001060.6 linkuse as main transcript	c.*680T>C		3_prime_UTR_variant	3/3	ENST00000375190.10	NP_001051.1	P21731-3Q05C92Q0VAB0
TBXA2R	NM_201636.3 linkuse as main transcript	c.1052T>C	p.Leu351Pro	missense_variant	4/4		NP_963998.2	P21731-2Q05C92Q0VAB0
TBXA2R	XM_011528214.3 linkuse as main transcript	c.*680T>C		3_prime_UTR_variant	4/4		XP_011526516.1	P21731-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TBXA2R	ENST00000375190 linkuse as main transcript	c.*680T>C		3_prime_UTR_variant	3/3	1	NM_001060.6	ENSP00000364336.4	P21731-3
TBXA2R	ENST00000589966 linkuse as main transcript	c.*543T>C		3_prime_UTR_variant	2/2	1		ENSP00000468145.1	K7ER80
TBXA2R	ENST00000411851.3 linkuse as main transcript	c.1052T>C	p.Leu351Pro	missense_variant	4/4	2		ENSP00000393333.2	P21731-2

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

15830

AN:

149250

Hom.:

908

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.0795

Gnomad AMR

AF:

0.0874

Gnomad ASJ

AF:

0.0667

Gnomad EAS

AF:

0.0228

Gnomad SAS

AF:

0.0807

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.100

Gnomad OTH

AF:

0.108

GnomAD3 exomes

AF:

0.0840

AC:

11530

AN:

137202

Hom.:

553

AF XY:

0.0848

AC XY:

6294

AN XY:

74252

show subpopulations

Gnomad AFR exome

AF:

0.135

Gnomad AMR exome

AF:

0.0552

Gnomad ASJ exome

AF:

0.0708

Gnomad EAS exome

AF:

0.0253

Gnomad SAS exome

AF:

0.0774

Gnomad FIN exome

AF:

0.121

Gnomad NFE exome

AF:

0.101

Gnomad OTH exome

AF:

0.100

GnomAD4 exome

AF:

0.0999

AC:

127038

AN:

1271112

Hom.:

6444

Cov.:

AF XY:

0.0999

AC XY:

62967

AN XY:

630406

show subpopulations

Gnomad4 AFR exome

AF:

0.147

Gnomad4 AMR exome

AF:

0.0627

Gnomad4 ASJ exome

AF:

0.0733

Gnomad4 EAS exome

AF:

0.0161

Gnomad4 SAS exome

AF:

0.0779

Gnomad4 FIN exome

AF:

0.128

Gnomad4 NFE exome

AF:

0.104

Gnomad4 OTH exome

AF:

0.0981

GnomAD4 genome

AF:

0.106

AC:

15832

AN:

149354

Hom.:

910

Cov.:

AF XY:

0.105

AC XY:

7654

AN XY:

72804

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.0873

Gnomad4 ASJ

AF:

0.0667

Gnomad4 EAS

AF:

0.0227

Gnomad4 SAS

AF:

0.0803

Gnomad4 FIN

AF:

0.115

Gnomad4 NFE

AF:

0.100

Gnomad4 OTH

AF:

0.107

Alfa

AF:

0.0505

Hom.:

Bravo

AF:

0.103

TwinsUK

AF:

0.103

AC:

383

ALSPAC

AF:

0.0999

AC:

385

ESP6500AA

AF:

0.106

AC:

187

ESP6500EA

AF:

0.0716

AC:

246

ExAC

AF:

0.0776

AC:

1664

Asia WGS

AF:

0.0520

AC:

180

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	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

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

-0.72

BayesDel_noAF

Benign

-0.68

CADD

Benign

5.4

DANN

Benign

0.92

Eigen

Benign

-0.76

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.0036

LIST_S2

Benign

0.66

MetaRNN

Benign

0.0020

MetaSVM

Benign

-1.0

PrimateAI

Uncertain

0.52

PROVEAN

Benign

0.27

REVEL

Benign

0.0050

Sift

Uncertain

0.025

Sift4G

Benign

0.29

Vest4

0.11

MPC

2.0

ClinPred

0.0048

GERP RS

0.23

gMVP

0.29

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