NM_001060.6:c.*680T>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001060.6(TBXA2R):c.*680T>C variant causes a 3 prime UTR 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. 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_001060.6 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.320

Publications

6 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 -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 rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6 link	c.*680T>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000375190.10	NP_001051.1	P21731-3Q05C92Q0VAB0
TBXA2R	NM_201636.3 link	c.1052T>C	p.Leu351Pro	missense_variant	Exon 4 of 4		NP_963998.2	P21731-2Q05C92Q0VAB0
TBXA2R	XM_011528214.3 link	c.*680T>C		3_prime_UTR_variant	Exon 4 of 4		XP_011526516.1	P21731-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TBXA2R	ENST00000375190.10 link	c.*680T>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_001060.6	ENSP00000364336.4	P21731-3
TBXA2R	ENST00000589966.1 link	c.*543T>C		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000468145.1	K7ER80
TBXA2R	ENST00000411851.3 link	c.1052T>C	p.Leu351Pro	missense_variant	Exon 4 of 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

GnomAD2 exomes

AF:

0.0840

AC:

11530

AN:

137202

AF XY:

0.0848

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 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

African (AFR)

AF:

0.147

AC:

4164

AN:

28326

American (AMR)

AF:

0.0627

AC:

2120

AN:

33804

Ashkenazi Jewish (ASJ)

AF:

0.0733

AC:

1644

AN:

22414

East Asian (EAS)

AF:

0.0161

AC:

504

AN:

31282

South Asian (SAS)

AF:

0.0779

AC:

6025

AN:

77384

European-Finnish (FIN)

AF:

0.128

AC:

3680

AN:

28734

Middle Eastern (MID)

AF:

0.141

AC:

631

AN:

4480

European-Non Finnish (NFE)

AF:

0.104

AC:

103164

AN:

992658

Other (OTH)

AF:

0.0981

AC:

5106

AN:

52030

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

5526

11052

16579

22105

27631

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3776

7552

11328

15104

18880

<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:

0.106

AC:

15832

AN:

149354

Hom.:

910

Cov.:

AF XY:

0.105

AC XY:

7654

AN XY:

72804

show subpopulations

African (AFR)

AF:

0.137

AC:

5520

AN:

40290

American (AMR)

AF:

0.0873

AC:

1297

AN:

14858

Ashkenazi Jewish (ASJ)

AF:

0.0667

AC:

231

AN:

3462

East Asian (EAS)

AF:

0.0227

AC:

115

AN:

5074

South Asian (SAS)

AF:

0.0803

AC:

374

AN:

4656

European-Finnish (FIN)

AF:

0.115

AC:

1169

AN:

10162

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.100

AC:

6789

AN:

67580

Other (OTH)

AF:

0.107

AC:

221

AN:

2072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

721

1442

2162

2883

3604

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<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:

0.0505

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

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_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.68

CADD

Benign

5.4

(source)

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

PhyloP100

0.32

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

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