chr19-3595704-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001060.6(TBXA2R):c.1016G>A(p.Arg339His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000754 in 1,590,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R339C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001060.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBXA2R | NM_001060.6 | c.1016G>A | p.Arg339His | missense_variant | 3/3 | ENST00000375190.10 | |
TBXA2R | XM_011528214.3 | c.1016G>A | p.Arg339His | missense_variant | 4/4 | ||
TBXA2R | NM_201636.3 | c.983+33G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBXA2R | ENST00000375190.10 | c.1016G>A | p.Arg339His | missense_variant | 3/3 | 1 | NM_001060.6 | P1 | |
TBXA2R | ENST00000589966.1 | c.627G>A | p.Ala209= | synonymous_variant | 2/2 | 1 | |||
TBXA2R | ENST00000411851.3 | c.983+33G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000342 AC: 7AN: 204756Hom.: 0 AF XY: 0.0000360 AC XY: 4AN XY: 111052
GnomAD4 exome AF: 0.00000695 AC: 10AN: 1438312Hom.: 0 Cov.: 66 AF XY: 0.00000561 AC XY: 4AN XY: 712956
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74492
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with TBXA2R-related conditions. This variant is present in population databases (rs563919263, gnomAD 0.02%). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 339 of the TBXA2R protein (p.Arg339His). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at