19-3595078-T-TAA

Position:

• chr19-3595078-T-TAA

Variant summary

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

The NM_001060.6(TBXA2R):​c.*609_*610insTT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.027 (70 hom., cov: 0)
  • Exomes 𝑓: 0.025 (1 hom.)
• Consequence: TBXA2R NM_001060.6 3_prime_UTR
• 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-TAA is Benign according to our data. Variant chr19-3595078-T-TAA is described in ClinVar as [Benign]. Clinvar id is 1285720.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.*609_*610insTT		3_prime_UTR_variant	3/3	ENST00000375190.10	NP_001051.1
TBXA2R	XM_011528214.3	c.*609_*610insTT		3_prime_UTR_variant	4/4		XP_011526516.1
TBXA2R	NM_201636.3	c.984-3_984-2insTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			NP_963998.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBXA2R	ENST00000375190.10	c.*609_*610insTT		3_prime_UTR_variant	3/3	1	NM_001060.6	ENSP00000364336	P1
TBXA2R	ENST00000589966.1	c.*472_*473insTT		3_prime_UTR_variant	2/2	1		ENSP00000468145
TBXA2R	ENST00000411851.3	c.984-3_984-2insTT		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		2		ENSP00000393333

Frequencies

GnomAD3 genomes AF: 0.0271 AC: 3504 AN: 129448 Hom.: 70 Cov.: 0

Gnomad AFR AF: 0.0543

Gnomad AMI AF: 0.0188

Gnomad AMR AF: 0.0148

Gnomad ASJ AF: 0.0278

Gnomad EAS AF: 0.000238

Gnomad SAS AF: 0.00358

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0338

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0183

GnomAD3 exomes AF: 0.0264 AC: 1057 AN: 40008 Hom.: 0 AF XY: 0.0255 AC XY: 518 AN XY: 20288

Gnomad AFR exome AF: 0.0585

Gnomad AMR exome AF: 0.0194

Gnomad ASJ exome AF: 0.0291

Gnomad EAS exome AF: 0.00691

Gnomad SAS exome AF: 0.0166

Gnomad FIN exome AF: 0.0176

Gnomad NFE exome AF: 0.0334

Gnomad OTH exome AF: 0.0307

GnomAD4 exome AF: 0.0250 AC: 8608 AN: 344588 Hom.: 1 Cov.: 0 AF XY: 0.0243 AC XY: 4438 AN XY: 182982

Gnomad4 AFR exome AF: 0.0458

Gnomad4 AMR exome AF: 0.0162

Gnomad4 ASJ exome AF: 0.0336

Gnomad4 EAS exome AF: 0.00398

Gnomad4 SAS exome AF: 0.0158

Gnomad4 FIN exome AF: 0.0254

Gnomad4 NFE exome AF: 0.0280

Gnomad4 OTH exome AF: 0.0269

GnomAD4 genome AF: 0.0271 AC: 3505 AN: 129458 Hom.: 70 Cov.: 0 AF XY: 0.0264 AC XY: 1626 AN XY: 61590

Gnomad4 AFR AF: 0.0543

Gnomad4 AMR AF: 0.0148

Gnomad4 ASJ AF: 0.0278

Gnomad4 EAS AF: 0.000238

Gnomad4 SAS AF: 0.00359

Gnomad4 FIN AF: 0.0121

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.0182

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 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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;