chr19-3600392-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001060.6(TBXA2R):c.243C>T(p.Thr81Thr) 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

Publications

13 publications found

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 Gene-Disease associations (from GenCC):

qualitative platelet defect
Inheritance: AD Classification: MODERATE Submitted by: ClinGen
bleeding diathesis due to thromboxane synthesis deficiency
Inheritance: Unknown, AD Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
schizophrenia
Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

TBXA2R links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6 link	c.243C>T	p.Thr81Thr	synonymous_variant	Exon 2 of 3	ENST00000375190.10	NP_001051.1	P21731-3Q05C92Q0VAB0
TBXA2R	NM_201636.3 link	c.243C>T	p.Thr81Thr	synonymous_variant	Exon 2 of 4		NP_963998.2	P21731-2Q05C92Q0VAB0
TBXA2R	XM_011528214.3 link	c.243C>T	p.Thr81Thr	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.243C>T	p.Thr81Thr	synonymous_variant	Exon 2 of 3	1	NM_001060.6	ENSP00000364336.4	P21731-3
TBXA2R	ENST00000589966.1 link	c.243C>T	p.Thr81Thr	synonymous_variant	Exon 1 of 2	1		ENSP00000468145.1	K7ER80
TBXA2R	ENST00000411851.3 link	c.243C>T	p.Thr81Thr	synonymous_variant	Exon 2 of 4	2		ENSP00000393333.2	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

GnomAD2 exomes

AF:

0.0814

AC:

20014

AN:

245816

AF XY:

0.0822

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 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

African (AFR)

AF:

0.140

AC:

4670

AN:

33464

American (AMR)

AF:

0.0550

AC:

2460

AN:

44704

Ashkenazi Jewish (ASJ)

AF:

0.0635

AC:

1657

AN:

26108

East Asian (EAS)

AF:

0.0166

AC:

660

AN:

39686

South Asian (SAS)

AF:

0.0640

AC:

5522

AN:

86254

European-Finnish (FIN)

AF:

0.0806

AC:

4270

AN:

53004

Middle Eastern (MID)

AF:

0.119

AC:

685

AN:

5762

European-Non Finnish (NFE)

AF:

0.100

AC:

111541

AN:

1111724

Other (OTH)

AF:

0.0883

AC:

5330

AN:

60360

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

9192

18384

27575

36767

45959

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4068

8136

12204

16272

20340

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.101

AC:

15317

AN:

152188

Hom.:

892

Cov.:

AF XY:

0.0981

AC XY:

7303

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.135

AC:

5602

AN:

41520

American (AMR)

AF:

0.0828

AC:

1266

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0649

AC:

225

AN:

3468

East Asian (EAS)

AF:

0.0241

AC:

125

AN:

5182

South Asian (SAS)

AF:

0.0682

AC:

329

AN:

4824

European-Finnish (FIN)

AF:

0.0778

AC:

824

AN:

10598

Middle Eastern (MID)

AF:

0.133

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0975

AC:

6631

AN:

67980

Other (OTH)

AF:

0.0965

AC:

204

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

708

1416

2123

2831

3539

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0962

Hom.:

393

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

Jul 09, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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

- -

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

-0.64

CADD

Benign

1.3

(source)

DANN

Benign

0.92

PhyloP100

-3.7

PromoterAI

-0.0043

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over