dbSNP rs34885751: TBXA2R:c.*604_*609delTTTTTT (chr19-3595078-TAAAAAA-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

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

The NM_201636.3(TBXA2R):c.984-8_984-3delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000287 in 348,218 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.0000029 ( 0 hom. )

Consequence

TBXA2R
NM_201636.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.320

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6 link	c.604_609delTTTTTT	3_prime_UTR_variant	Exon 3 of 3	ENST00000375190.10	NP_001051.1	P21731-3Q05C92Q0VAB0
TBXA2R	XM_011528214.3 link	c.604_609delTTTTTT	3_prime_UTR_variant	Exon 4 of 4		XP_011526516.1	P21731-3
TBXA2R	NM_201636.3 link	c.984-8_984-3delTTTTTT	splice_region_variant, intron_variant	Intron 3 of 3		NP_963998.2	P21731-2Q05C92Q0VAB0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TBXA2R	ENST00000375190 link	c.604_609delTTTTTT	3_prime_UTR_variant	Exon 3 of 3	1	NM_001060.6	ENSP00000364336.4	P21731-3
TBXA2R	ENST00000589966 link	c.467_472delTTTTTT	3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000468145.1	K7ER80
TBXA2R	ENST00000411851.3 link	c.984-8_984-3delTTTTTT	splice_region_variant, intron_variant	Intron 3 of 3	2		ENSP00000393333.2	P21731-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000287

AC:

AN:

348218

Hom.:

AF XY:

0.00

AC XY:

AN XY:

184930

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000456

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over