Genetic Variant NM_001060.6:c.*654G>A (chr19-3595034-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001060.6(TBXA2R):c.*654G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 1,123,478 control chromosomes in the GnomAD database, including 142,113 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.46 ( 15501 hom., cov: 25)

Exomes 𝑓: 0.50 ( 126612 hom. )

Consequence

TBXA2R
NM_001060.6 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.95

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BP6

Variant 19-3595034-C-T is Benign according to our data. Variant chr19-3595034-C-T is described in ClinVar as [Benign]. Clinvar id is 263264.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6 link	c.*654G>A		3_prime_UTR_variant	Exon 3 of 3	ENST00000375190.10	NP_001051.1	P21731-3Q05C92Q0VAB0
TBXA2R	NM_201636.3 link	c.1026G>A	p.Thr342Thr	synonymous_variant	Exon 4 of 4		NP_963998.2	P21731-2Q05C92Q0VAB0
TBXA2R	XM_011528214.3 link	c.*654G>A		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 link	c.*654G>A		3_prime_UTR_variant	Exon 3 of 3	1	NM_001060.6	ENSP00000364336.4	P21731-3
TBXA2R	ENST00000589966 link	c.*517G>A		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000468145.1	K7ER80
TBXA2R	ENST00000411851.3 link	c.1026G>A	p.Thr342Thr	synonymous_variant	Exon 4 of 4	2		ENSP00000393333.2	P21731-2

Frequencies

GnomAD3 genomes

AF:

0.461

AC:

65582

AN:

142368

Hom.:

15496

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.339

Gnomad AMR

AF:

0.428

Gnomad ASJ

AF:

0.555

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.583

Gnomad NFE

AF:

0.547

Gnomad OTH

AF:

0.499

GnomAD3 exomes

AF:

0.426

AC:

56865

AN:

133342

Hom.:

13295

AF XY:

0.431

AC XY:

31231

AN XY:

72442

show subpopulations

Gnomad AFR exome

AF:

0.305

Gnomad AMR exome

AF:

0.321

Gnomad ASJ exome

AF:

0.539

Gnomad EAS exome

AF:

0.145

Gnomad SAS exome

AF:

0.373

Gnomad FIN exome

AF:

0.500

Gnomad NFE exome

AF:

0.542

Gnomad OTH exome

AF:

0.477

GnomAD4 exome

AF:

0.501

AC:

491742

AN:

981030

Hom.:

126612

Cov.:

AF XY:

0.498

AC XY:

248368

AN XY:

499166

show subpopulations

Gnomad4 AFR exome

AF:

0.324

Gnomad4 AMR exome

AF:

0.339

Gnomad4 ASJ exome

AF:

0.548

Gnomad4 EAS exome

AF:

0.141

Gnomad4 SAS exome

AF:

0.370

Gnomad4 FIN exome

AF:

0.512

Gnomad4 NFE exome

AF:

0.540

Gnomad4 OTH exome

AF:

0.483

GnomAD4 genome

AF:

0.461

AC:

65601

AN:

142448

Hom.:

15501

Cov.:

AF XY:

0.456

AC XY:

31557

AN XY:

69276

show subpopulations

Gnomad4 AFR

AF:

0.339

Gnomad4 AMR

AF:

0.428

Gnomad4 ASJ

AF:

0.555

Gnomad4 EAS

AF:

0.160

Gnomad4 SAS

AF:

0.379

Gnomad4 FIN

AF:

0.523

Gnomad4 NFE

AF:

0.547

Gnomad4 OTH

AF:

0.498

Alfa

AF:

0.495

Hom.:

3419

Bravo

AF:

0.427

Asia WGS

AF:

0.289

AC:

1008

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

This variant is associated with the following publications: (PMID: 16953279) -

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

-1.0

CADD

Benign

0.68

DANN

Benign

0.76

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