rs4523

Variant names:

• chr19-3595796-A-C
• NM_001060.6:c.924T>G

Your query was ambiguous. Multiple possible variants found:

• chr19-3595796-A-C
• chr19-3595796-A-G
• chr19-3595796-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001060.6(TBXA2R):​c.924T>G​(p.Tyr308*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Y308Y) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TBXA2R NM_001060.6 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.82

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.924T>G	p.Tyr308*	stop_gained	Exon 3 of 3	ENST00000375190.10	NP_001051.1
TBXA2R	NM_201636.3	c.924T>G	p.Tyr308*	stop_gained	Exon 3 of 4		NP_963998.2
TBXA2R	XM_011528214.3	c.924T>G	p.Tyr308*	stop_gained	Exon 4 of 4		XP_011526516.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBXA2R	ENST00000375190.10	c.924T>G	p.Tyr308*	stop_gained	Exon 3 of 3	1	NM_001060.6	ENSP00000364336.4
TBXA2R	ENST00000589966.1	c.535T>G	p.Tyr179Asp	missense_variant	Exon 2 of 2	1		ENSP00000468145.1
TBXA2R	ENST00000411851.3	c.924T>G	p.Tyr308*	stop_gained	Exon 3 of 4	2		ENSP00000393333.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 103

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.058	T
BayesDel_noAF	Benign	-0.32
CADD	Pathogenic	41
DANN	Uncertain	1.0
Eigen	Uncertain	0.45
Eigen_PC	Uncertain	0.30
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Benign	0.14	T
MetaRNN	Benign	0.31	T
Sift4G	Benign	0.19	T
Vest4		0.36
MVP		0.46
GERP RS		3.1

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-3595794;