19-3595078-TAAAAAA-TAAAAA

Variant names:

• chr19-3595078-TA-T
• rs34885751
• NM_001060.6:c.*609delT

Variant summary

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

The NM_201636.3(TBXA2R):​c.984-3delT 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 0.0088 (7 hom., cov: 0)
  • Exomes 𝑓: 0.21 (0 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-TA-T is Benign according to our data. Variant chr19-3595078-TA-T is described in ClinVar as [Benign]. Clinvar id is 1239007.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.*609delT		3_prime_UTR_variant	Exon 3 of 3	ENST00000375190.10	NP_001051.1
TBXA2R	XM_011528214.3	c.*609delT		3_prime_UTR_variant	Exon 4 of 4		XP_011526516.1
TBXA2R	NM_201636.3	c.984-3delT		splice_region_variant, intron_variant	Intron 3 of 3		NP_963998.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBXA2R	ENST00000375190	c.*609delT		3_prime_UTR_variant	Exon 3 of 3	1	NM_001060.6	ENSP00000364336.4
TBXA2R	ENST00000589966	c.*472delT		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000468145.1
TBXA2R	ENST00000411851.3	c.984-3delT		splice_region_variant, intron_variant	Intron 3 of 3	2		ENSP00000393333.2

Frequencies

GnomAD3 genomes AF: 0.00873 AC: 1130 AN: 129432 Hom.: 7 Cov.: 0

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00704

Gnomad ASJ AF: 0.00216

Gnomad EAS AF: 0.00190

Gnomad SAS AF: 0.00102

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00149

Gnomad OTH AF: 0.00742

GnomAD3 exomes AF: 0.277 AC: 11065 AN: 40008 Hom.: 0 AF XY: 0.276 AC XY: 5597 AN XY: 20288

Gnomad AFR exome AF: 0.203

Gnomad AMR exome AF: 0.312

Gnomad ASJ exome AF: 0.232

Gnomad EAS exome AF: 0.386

Gnomad SAS exome AF: 0.305

Gnomad FIN exome AF: 0.284

Gnomad NFE exome AF: 0.228

Gnomad OTH exome AF: 0.243

GnomAD4 exome AF: 0.210 AC: 71111 AN: 339270 Hom.: 0 Cov.: 0 AF XY: 0.213 AC XY: 38317 AN XY: 179904

Gnomad4 AFR exome AF: 0.186

Gnomad4 AMR exome AF: 0.264

Gnomad4 ASJ exome AF: 0.199

Gnomad4 EAS exome AF: 0.319

Gnomad4 SAS exome AF: 0.259

Gnomad4 FIN exome AF: 0.202

Gnomad4 NFE exome AF: 0.189

Gnomad4 OTH exome AF: 0.205

GnomAD4 genome AF: 0.00877 AC: 1135 AN: 129442 Hom.: 7 Cov.: 0 AF XY: 0.00862 AC XY: 531 AN XY: 61574

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.00720

Gnomad4 ASJ AF: 0.00216

Gnomad4 EAS AF: 0.00191

Gnomad4 SAS AF: 0.000770

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.00149

Gnomad4 OTH AF: 0.00740

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 05, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;