19-3595078-TAAAAAA-TAAAAAAAAA

Variant names:

• chr19-3595078-T-TAAA
• rs34885751
• NM_001060.6:c.*607_*609dupTTT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_201636.3(TBXA2R):​c.984-5_984-3dupTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000031 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0018 (0 hom.)
• Consequence: TBXA2R NM_201636.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 615 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.*607_*609dupTTT		3_prime_UTR_variant	Exon 3 of 3	ENST00000375190.10	NP_001051.1
TBXA2R	XM_011528214.3	c.*607_*609dupTTT		3_prime_UTR_variant	Exon 4 of 4		XP_011526516.1
TBXA2R	NM_201636.3	c.984-5_984-3dupTTT		splice_region_variant, 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.*607_*609dupTTT		3_prime_UTR_variant	Exon 3 of 3	1	NM_001060.6	ENSP00000364336.4
TBXA2R	ENST00000589966	c.*470_*472dupTTT		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000468145.1
TBXA2R	ENST00000411851.3	c.984-5_984-3dupTTT		splice_region_variant, intron_variant	Intron 3 of 3	2		ENSP00000393333.2

Frequencies

GnomAD3 genomes AF: 0.0000309 AC: 4 AN: 129498 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000791

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000298

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000162

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00230 AC: 92 AN: 40008 Hom.: 0 AF XY: 0.00242 AC XY: 49 AN XY: 20288

Gnomad AFR exome AF: 0.00556

Gnomad AMR exome AF: 0.00154

Gnomad ASJ exome AF: 0.00453

Gnomad EAS exome AF: 0.000545

Gnomad SAS exome AF: 0.00164

Gnomad FIN exome AF: 0.00147

Gnomad NFE exome AF: 0.00261

Gnomad OTH exome AF: 0.00307

GnomAD4 exome AF: 0.00177 AC: 615 AN: 347316 Hom.: 0 Cov.: 0 AF XY: 0.00177 AC XY: 326 AN XY: 184456

Gnomad4 AFR exome AF: 0.00389

Gnomad4 AMR exome AF: 0.00109

Gnomad4 ASJ exome AF: 0.00263

Gnomad4 EAS exome AF: 0.0000496

Gnomad4 SAS exome AF: 0.00120

Gnomad4 FIN exome AF: 0.00176

Gnomad4 NFE exome AF: 0.00198

Gnomad4 OTH exome AF: 0.00174

GnomAD4 genome AF: 0.0000309 AC: 4 AN: 129498 Hom.: 0 Cov.: 0 AF XY: 0.0000487 AC XY: 3 AN XY: 61574

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000791

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000298

Gnomad4 NFE AF: 0.0000162

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34885751; hg19: chr19-3595076;