Variant 19-3595524-G-A 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_001060.6(TBXA2R):c.*164C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,434,332 control chromosomes in the GnomAD database, including 9,609 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1197 hom., cov: 33)

Exomes 𝑓: 0.11 ( 8412 hom. )

Consequence

TBXA2R
NM_001060.6 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.129

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 (BayesDel_noAF=-0.87).

BP6

Variant 19-3595524-G-A is Benign according to our data. Variant chr19-3595524-G-A is described in ClinVar as [Benign]. Clinvar id is 1297313.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
TBXA2R	NM_001060.6 linkuse as main transcript	c.*164C>T	3_prime_UTR_variant	3/3	ENST00000375190.10	NP_001051.1
TBXA2R	XM_011528214.3 linkuse as main transcript	c.*164C>T	3_prime_UTR_variant	4/4		XP_011526516.1
TBXA2R	NM_201636.3 linkuse as main transcript	c.983+213C>T	intron_variant			NP_963998.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBXA2R	ENST00000375190.10 linkuse as main transcript	c.*164C>T	3_prime_UTR_variant	3/3	1	NM_001060.6	ENSP00000364336	P1	P21731-3
TBXA2R	ENST00000589966.1 linkuse as main transcript	c.*27C>T	3_prime_UTR_variant	2/2	1		ENSP00000468145
TBXA2R	ENST00000411851.3 linkuse as main transcript	c.983+213C>T	intron_variant		2		ENSP00000393333		P21731-2

Frequencies

GnomAD3 genomes

AF:

0.118

AC:

17937

AN:

152130

Hom.:

1196

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.0994

Gnomad ASJ

AF:

0.0720

Gnomad EAS

AF:

0.0220

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.114

Gnomad OTH

AF:

0.120

GnomAD3 exomes

AF:

0.0972

AC:

6037

AN:

62100

Hom.:

331

AF XY:

0.0981

AC XY:

3058

AN XY:

31166

show subpopulations

Gnomad AFR exome

AF:

0.148

Gnomad AMR exome

AF:

0.0761

Gnomad ASJ exome

AF:

0.0705

Gnomad EAS exome

AF:

0.0266

Gnomad SAS exome

AF:

0.105

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.114

Gnomad OTH exome

AF:

0.109

GnomAD4 exome

AF:

0.113

AC:

144349

AN:

1282084

Hom.:

8412

Cov.:

AF XY:

0.113

AC XY:

69971

AN XY:

620346

show subpopulations

Gnomad4 AFR exome

AF:

0.150

Gnomad4 AMR exome

AF:

0.0800

Gnomad4 ASJ exome

AF:

0.0725

Gnomad4 EAS exome

AF:

0.0146

Gnomad4 SAS exome

AF:

0.110

Gnomad4 FIN exome

AF:

0.124

Gnomad4 NFE exome

AF:

0.116

Gnomad4 OTH exome

AF:

0.106

GnomAD4 genome

AF:

0.118

AC:

17938

AN:

152248

Hom.:

1197

Cov.:

AF XY:

0.116

AC XY:

8657

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.146

Gnomad4 AMR

AF:

0.0993

Gnomad4 ASJ

AF:

0.0720

Gnomad4 EAS

AF:

0.0218

Gnomad4 SAS

AF:

0.107

Gnomad4 FIN

AF:

0.122

Gnomad4 NFE

AF:

0.114

Gnomad4 OTH

AF:

0.118

Alfa

AF:

0.111

Hom.:

1237

Bravo

AF:

0.116

Asia WGS

AF:

0.0680

AC:

236

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

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: 21677697) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.7

DANN

Benign

0.69

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