ENST00000589966.1:c.628C>G

Variant names:

• chr19-3595703-G-C
• ENST00000589966.1:c.628C>G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Moderate BP6_Moderate

The ENST00000589966.1(TBXA2R):​c.628C>G​(p.Leu210Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: TBXA2R ENST00000589966.1 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0970

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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17487812).
• BP6: Variant 19-3595703-G-C is Benign according to our data. Variant chr19-3595703-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 3699884.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBXA2R	NM_001060.6	c.1017C>G	p.Arg339Arg	synonymous_variant	Exon 3 of 3	ENST00000375190.10	NP_001051.1
TBXA2R	XM_011528214.3	c.1017C>G	p.Arg339Arg	synonymous_variant	Exon 4 of 4		XP_011526516.1
TBXA2R	NM_201636.3	c.983+34C>G		intron_variant	Intron 3 of 3		NP_963998.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBXA2R	ENST00000589966.1	c.628C>G	p.Leu210Val	missense_variant	Exon 2 of 2	1		ENSP00000468145.1
TBXA2R	ENST00000375190.10	c.1017C>G	p.Arg339Arg	synonymous_variant	Exon 3 of 3	1	NM_001060.6	ENSP00000364336.4
TBXA2R	ENST00000411851.3	c.983+34C>G		intron_variant	Intron 3 of 3	2		ENSP00000393333.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 65

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 11, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	2.0
DANN	Benign	0.62
FATHMM_MKL	Benign	0.049	N
LIST_S2	Benign	0.32	T
M_CAP	Benign	0.0099	T
MetaRNN	Benign	0.17	T
Sift4G	Benign	0.31	T
Vest4		0.17
MVP		0.67
GERP RS		-2.0

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: chr19-3595701;