Variant 19-3600392-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001060.6(TBXA2R):c.243C>T(p.Thr81=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0943 in 1,613,254 control chromosomes in the GnomAD database, including 7,579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 892 hom., cov: 32)

Exomes 𝑓: 0.094 ( 6687 hom. )

Consequence

TBXA2R
NM_001060.6 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.73

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 19-3600392-G-A is Benign according to our data. Variant chr19-3600392-G-A is described in ClinVar as [Benign]. Clinvar id is 263266.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.73 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TBXA2R	NM_001060.6 linkuse as main transcript	c.243C>T	p.Thr81=	synonymous_variant	2/3	ENST00000375190.10
TBXA2R	NM_201636.3 linkuse as main transcript	c.243C>T	p.Thr81=	synonymous_variant	2/4
TBXA2R	XM_011528214.3 linkuse as main transcript	c.243C>T	p.Thr81=	synonymous_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBXA2R	ENST00000375190.10 linkuse as main transcript	c.243C>T	p.Thr81=	synonymous_variant	2/3	1	NM_001060.6	P1	P21731-3
TBXA2R	ENST00000589966.1 linkuse as main transcript	c.243C>T	p.Thr81=	synonymous_variant	1/2	1
TBXA2R	ENST00000411851.3 linkuse as main transcript	c.243C>T	p.Thr81=	synonymous_variant	2/4	2			P21731-2

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15313

AN:

152070

Hom.:

891

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.0791

Gnomad AMR

AF:

0.0829

Gnomad ASJ

AF:

0.0649

Gnomad EAS

AF:

0.0245

Gnomad SAS

AF:

0.0684

Gnomad FIN

AF:

0.0778

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.0976

Gnomad OTH

AF:

0.0975

GnomAD3 exomes

AF:

0.0814

AC:

20014

AN:

245816

Hom.:

929

AF XY:

0.0822

AC XY:

11017

AN XY:

134074

show subpopulations

Gnomad AFR exome

AF:

0.138

Gnomad AMR exome

AF:

0.0505

Gnomad ASJ exome

AF:

0.0658

Gnomad EAS exome

AF:

0.0264

Gnomad SAS exome

AF:

0.0637

Gnomad FIN exome

AF:

0.0829

Gnomad NFE exome

AF:

0.0976

Gnomad OTH exome

AF:

0.0907

GnomAD4 exome

AF:

0.0936

AC:

136795

AN:

1461066

Hom.:

6687

Cov.:

AF XY:

0.0933

AC XY:

67785

AN XY:

726864

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.0550

Gnomad4 ASJ exome

AF:

0.0635

Gnomad4 EAS exome

AF:

0.0166

Gnomad4 SAS exome

AF:

0.0640

Gnomad4 FIN exome

AF:

0.0806

Gnomad4 NFE exome

AF:

0.100

Gnomad4 OTH exome

AF:

0.0883

GnomAD4 genome

AF:

0.101

AC:

15317

AN:

152188

Hom.:

892

Cov.:

AF XY:

0.0981

AC XY:

7303

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.0828

Gnomad4 ASJ

AF:

0.0649

Gnomad4 EAS

AF:

0.0241

Gnomad4 SAS

AF:

0.0682

Gnomad4 FIN

AF:

0.0778

Gnomad4 NFE

AF:

0.0975

Gnomad4 OTH

AF:

0.0965

Alfa

AF:

0.0959

Hom.:

280

Bravo

AF:

0.102

Asia WGS

AF:

0.0450

AC:

157

AN:

3478

EpiCase

AF:

0.102

EpiControl

AF:

0.106

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
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_noAF

Benign

-0.64

CADD

Benign

1.3

DANN

Benign

0.92

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