rs2238634

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000375190.10(TBXA2R):​c.-84+1799T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,138 control chromosomes in the GnomAD database, including 50,434 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 0.81 ( 50434 hom., cov: 32)

Consequence

TBXA2R
ENST00000375190.10 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.491
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TBXA2RNM_001060.6 linkuse as main transcriptc.-84+1799T>G intron_variant ENST00000375190.10 NP_001051.1
TBXA2RNM_201636.3 linkuse as main transcriptc.-84+1799T>G intron_variant NP_963998.2
TBXA2RXM_011528214.3 linkuse as main transcriptc.-202+1799T>G intron_variant XP_011526516.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TBXA2RENST00000375190.10 linkuse as main transcriptc.-84+1799T>G intron_variant 1 NM_001060.6 ENSP00000364336 P1P21731-3
TBXA2RENST00000411851.3 linkuse as main transcriptc.-84+1799T>G intron_variant 2 ENSP00000393333 P21731-2

Frequencies

GnomAD3 genomes
AF:
0.812
AC:
123423
AN:
152020
Hom.:
50390
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.882
Gnomad AMI
AF:
0.743
Gnomad AMR
AF:
0.752
Gnomad ASJ
AF:
0.876
Gnomad EAS
AF:
0.774
Gnomad SAS
AF:
0.664
Gnomad FIN
AF:
0.777
Gnomad MID
AF:
0.921
Gnomad NFE
AF:
0.798
Gnomad OTH
AF:
0.828
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.812
AC:
123519
AN:
152138
Hom.:
50434
Cov.:
32
AF XY:
0.807
AC XY:
60049
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.882
Gnomad4 AMR
AF:
0.752
Gnomad4 ASJ
AF:
0.876
Gnomad4 EAS
AF:
0.774
Gnomad4 SAS
AF:
0.664
Gnomad4 FIN
AF:
0.777
Gnomad4 NFE
AF:
0.798
Gnomad4 OTH
AF:
0.820
Alfa
AF:
0.803
Hom.:
5727
Bravo
AF:
0.818
Asia WGS
AF:
0.669
AC:
2328
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.0
DANN
Benign
0.75

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

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

Other links and lift over

dbSNP: rs2238634; hg19: chr19-3604729; API