19-3595078-T-TA

Position:

• chr19-3595078-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_201636.3(TBXA2R):​c.984-3dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.42 (11618 hom., cov: 0)
  • Exomes 𝑓: 0.23 (111 hom.)
• Consequence: TBXA2R NM_201636.3 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.94

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 19-3595078-T-TA is Benign according to our data. Variant chr19-3595078-T-TA is described in ClinVar as [Benign]. Clinvar id is 1240852.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.*609dupT		3_prime_UTR_variant	3/3	ENST00000375190.10	NP_001051.1
TBXA2R	XM_011528214.3	c.*609dupT		3_prime_UTR_variant	4/4		XP_011526516.1
TBXA2R	NM_201636.3	c.984-3dupT		splice_region_variant, intron_variant			NP_963998.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBXA2R	ENST00000375190	c.*609dupT		3_prime_UTR_variant	3/3	1	NM_001060.6	ENSP00000364336.4
TBXA2R	ENST00000589966	c.*472dupT		3_prime_UTR_variant	2/2	1		ENSP00000468145.1
TBXA2R	ENST00000411851.3	c.984-3dupT		splice_region_variant, intron_variant		2		ENSP00000393333.2

Frequencies

GnomAD3 genomes AF: 0.423 AC: 54650 AN: 129266 Hom.: 11618 Cov.: 0

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.0740

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.446

GnomAD3 exomes AF: 0.214 AC: 8545 AN: 40008 Hom.: 10 AF XY: 0.215 AC XY: 4370 AN XY: 20288

Gnomad AFR exome AF: 0.304

Gnomad AMR exome AF: 0.175

Gnomad ASJ exome AF: 0.260

Gnomad EAS exome AF: 0.0804

Gnomad SAS exome AF: 0.168

Gnomad FIN exome AF: 0.191

Gnomad NFE exome AF: 0.274

Gnomad OTH exome AF: 0.255

GnomAD4 exome AF: 0.227 AC: 78213 AN: 344546 Hom.: 111 Cov.: 0 AF XY: 0.223 AC XY: 40867 AN XY: 182998

Gnomad4 AFR exome AF: 0.269

Gnomad4 AMR exome AF: 0.165

Gnomad4 ASJ exome AF: 0.237

Gnomad4 EAS exome AF: 0.0741

Gnomad4 SAS exome AF: 0.172

Gnomad4 FIN exome AF: 0.241

Gnomad4 NFE exome AF: 0.253

Gnomad4 OTH exome AF: 0.232

GnomAD4 genome AF: 0.423 AC: 54652 AN: 129276 Hom.: 11618 Cov.: 0 AF XY: 0.415 AC XY: 25546 AN XY: 61514

Gnomad4 AFR AF: 0.465

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.0743

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.447

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 05, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs34885751; hg19: chr19-3595076;