rs2238633

Variant names:

• chr19-3604551-C-A
• rs2238633
• NM_001060.6:c.-84+1979G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-3604551-C-A
• chr19-3604551-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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 Gene-Disease associations (from GenCC):

• qualitative platelet defect

  Inheritance: AD Classification: MODERATE Submitted by: ClinGen
• bleeding diathesis due to thromboxane synthesis deficiency

  Inheritance: Unknown, AD Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.-84+1979G>T		intron_variant	Intron 1 of 2	ENST00000375190.10	NP_001051.1
TBXA2R	NM_201636.3	c.-84+1979G>T		intron_variant	Intron 1 of 3		NP_963998.2
TBXA2R	XM_011528214.3	c.-201-1819G>T		intron_variant	Intron 1 of 3		XP_011526516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBXA2R	ENST00000375190.10	c.-84+1979G>T		intron_variant	Intron 1 of 2	1	NM_001060.6	ENSP00000364336.4
TBXA2R	ENST00000411851.3	c.-84+1979G>T		intron_variant	Intron 1 of 3	2		ENSP00000393333.2

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

African (AFR) AF: 0.0942 AC: 3907 AN: 41476

American (AMR) AF: 0.234 AC: 3578 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2697 AN: 5136

South Asian (SAS) AF: 0.165 AC: 792 AN: 4812

European-Finnish (FIN) AF: 0.145 AC: 1540 AN: 10604

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10374 AN: 67960

Other (OTH) AF: 0.164 AC: 347 AN: 2114

Alfa AF: 0.157 Hom.: 3177

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
PhyloP100		0.043
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2238633; hg19: chr19-3604549;