19-3595078-TAAAAAA-TAAA

Variant names:

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

Variant summary

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

The NM_201636.3(TBXA2R):​c.984-5_984-3delTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00304 in 474,752 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000015 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0042 (0 hom.)
• Consequence: TBXA2R NM_201636.3 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

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 1443 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.0000154 AC: 2 AN: 129476 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000149

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000162

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00467 AC: 187 AN: 40008 Hom.: 0 AF XY: 0.00419 AC XY: 85 AN XY: 20288

Gnomad AFR exome AF: 0.00381

Gnomad AMR exome AF: 0.00538

Gnomad ASJ exome AF: 0.00776

Gnomad EAS exome AF: 0.00364

Gnomad SAS exome AF: 0.00796

Gnomad FIN exome AF: 0.00735

Gnomad NFE exome AF: 0.00353

Gnomad OTH exome AF: 0.00307

GnomAD4 exome AF: 0.00418 AC: 1443 AN: 345276 Hom.: 0 AF XY: 0.00403 AC XY: 739 AN XY: 183294

Gnomad4 AFR exome AF: 0.00426

Gnomad4 AMR exome AF: 0.00502

Gnomad4 ASJ exome AF: 0.00600

Gnomad4 EAS exome AF: 0.00536

Gnomad4 SAS exome AF: 0.00361

Gnomad4 FIN exome AF: 0.00476

Gnomad4 NFE exome AF: 0.00403

Gnomad4 OTH exome AF: 0.00397

GnomAD4 genome AF: 0.0000154 AC: 2 AN: 129476 Hom.: 0 Cov.: 0 AF XY: 0.0000162 AC XY: 1 AN XY: 61562

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000149

Gnomad4 NFE AF: 0.0000162

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs34885751; hg19: chr19-3595076;