rs2238633

chr19-3604551-C-Achr19-3604551-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001060.6(TBXA2R):c.-84+1979G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,044 control chromosomes in the GnomAD database, including 2,532 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2532 hom., cov: 31)
• Consequence: TBXA2R NM_001060.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBXA2R	NM_001060.6	c.-84+1979G>T		intron_variant		ENST00000375190.10
TBXA2R	NM_201636.3	c.-84+1979G>T		intron_variant
TBXA2R	XM_011528214.3	c.-201-1819G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBXA2R	ENST00000375190.10	c.-84+1979G>T		intron_variant		1	NM_001060.6	P1
TBXA2R	ENST00000411851.3	c.-84+1979G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24352 AN: 151928 Hom.: 2530 Cov.: 31

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.166

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.160 AC: 24356 AN: 152044 Hom.: 2532 Cov.: 31 AF XY: 0.162 AC XY: 12058 AN XY: 74310

Gnomad4 AFR AF: 0.0942

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.164

Alfa AF: 0.155 Hom.: 2389

Bravo AF: 0.173

Asia WGS AF: 0.274 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.5
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

Other links and lift over

dbSNP: rs2238633; hg19: chr19-3604549;