19-3604301-T-C

Variant names:

• chr19-3604301-T-C
• rs2238631
• NM_001060.6:c.-84+2229A>G

Variant summary

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

The NM_001060.6(TBXA2R):​c.-84+2229A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,030 control chromosomes in the GnomAD database, including 53,493 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 0.83 (53493 hom., cov: 32)
• Consequence: TBXA2R NM_001060.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.-84+2229A>G		intron_variant	Intron 1 of 2	ENST00000375190.10	NP_001051.1
TBXA2R	NM_201636.3	c.-84+2229A>G		intron_variant	Intron 1 of 3		NP_963998.2
TBXA2R	XM_011528214.3	c.-201-1569A>G		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+2229A>G		intron_variant	Intron 1 of 2	1	NM_001060.6	ENSP00000364336.4
TBXA2R	ENST00000411851.3	c.-84+2229A>G		intron_variant	Intron 1 of 3	2		ENSP00000393333.2

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126713 AN: 151912 Hom.: 53447 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.834 AC: 126809 AN: 152030 Hom.: 53493 Cov.: 32 AF XY: 0.829 AC XY: 61603 AN XY: 74290

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.767

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.833

Alfa AF: 0.808 Hom.: 60177

Bravo AF: 0.843

Asia WGS AF: 0.674 AC: 2343 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.9
DANN	Benign	0.24

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: rs2238631; hg19: chr19-3604299;