NM_001060.6:c.*164C>T

Variant names:

• chr19-3595524-G-A
• rs13306046
• NM_001060.6:c.*164C>T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001060.6(TBXA2R):​c.*164C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,434,332 control chromosomes in the GnomAD database, including 9,609 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.12 (1197 hom., cov: 33)
  • Exomes 𝑓: 0.11 (8412 hom.)
• Consequence: TBXA2R NM_001060.6 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.129

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 19-3595524-G-A is Benign according to our data. Variant chr19-3595524-G-A is described in ClinVar as [Benign]. Clinvar id is 1297313.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.*164C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000375190.10	NP_001051.1
TBXA2R	XM_011528214.3	c.*164C>T		3_prime_UTR_variant	Exon 4 of 4		XP_011526516.1
TBXA2R	NM_201636.3	c.983+213C>T		intron_variant	Intron 3 of 3		NP_963998.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBXA2R	ENST00000375190	c.*164C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_001060.6	ENSP00000364336.4
TBXA2R	ENST00000589966	c.*27C>T		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000468145.1
TBXA2R	ENST00000411851.3	c.983+213C>T		intron_variant	Intron 3 of 3	2		ENSP00000393333.2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17937 AN: 152130 Hom.: 1196 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.0220

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.120

GnomAD3 exomes AF: 0.0972 AC: 6037 AN: 62100 Hom.: 331 AF XY: 0.0981 AC XY: 3058 AN XY: 31166

Gnomad AFR exome AF: 0.148

Gnomad AMR exome AF: 0.0761

Gnomad ASJ exome AF: 0.0705

Gnomad EAS exome AF: 0.0266

Gnomad SAS exome AF: 0.105

Gnomad FIN exome AF: 0.110

Gnomad NFE exome AF: 0.114

Gnomad OTH exome AF: 0.109

GnomAD4 exome AF: 0.113 AC: 144349 AN: 1282084 Hom.: 8412 Cov.: 55 AF XY: 0.113 AC XY: 69971 AN XY: 620346

Gnomad4 AFR exome AF: 0.150

Gnomad4 AMR exome AF: 0.0800

Gnomad4 ASJ exome AF: 0.0725

Gnomad4 EAS exome AF: 0.0146

Gnomad4 SAS exome AF: 0.110

Gnomad4 FIN exome AF: 0.124

Gnomad4 NFE exome AF: 0.116

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.118 AC: 17938 AN: 152248 Hom.: 1197 Cov.: 33 AF XY: 0.116 AC XY: 8657 AN XY: 74454

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.0993

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.0218

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.118

Alfa AF: 0.111 Hom.: 1237

Bravo AF: 0.116

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 21677697) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.69

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: rs13306046; hg19: chr19-3595522; COSMIC: COSV59258917; COSMIC: COSV59258917;