19-3595078-TAAAAAA-TAA

Variant names:

• chr19-3595078-TAAAA-T
• NM_001060.6:c.*606_*609delTTTT

Variant summary

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

The NM_201636.3(TBXA2R):​c.984-6_984-3delTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000653 in 347,582 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 0.0 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00065 (0 hom.)
  • Failed GnomAD Quality Control
• 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 227 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.*606_*609delTTTT		3_prime_UTR_variant	Exon 3 of 3	ENST00000375190.10	NP_001051.1
TBXA2R	XM_011528214.3	c.*606_*609delTTTT		3_prime_UTR_variant	Exon 4 of 4		XP_011526516.1
TBXA2R	NM_201636.3	c.984-6_984-3delTTTT		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.*606_*609delTTTT		3_prime_UTR_variant	Exon 3 of 3	1	NM_001060.6	ENSP00000364336.4
TBXA2R	ENST00000589966	c.*469_*472delTTTT		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000468145.1
TBXA2R	ENST00000411851.3	c.984-6_984-3delTTTT		splice_region_variant, intron_variant	Intron 3 of 3	2		ENSP00000393333.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 129498 Hom.: 0 Cov.: 0 FAILED QC

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: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000653 AC: 227 AN: 347582 Hom.: 0 AF XY: 0.000607 AC XY: 112 AN XY: 184590

Gnomad4 AFR exome AF: 0.000353

Gnomad4 AMR exome AF: 0.000788

Gnomad4 ASJ exome AF: 0.000916

Gnomad4 EAS exome AF: 0.00114

Gnomad4 SAS exome AF: 0.000480

Gnomad4 FIN exome AF: 0.000945

Gnomad4 NFE exome AF: 0.000603

Gnomad4 OTH exome AF: 0.000814

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 129498 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 61574

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: 0.00

Gnomad4 NFE AF: 0.00

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-3595076;