NM_001060.6:c.*715C>T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001060.6(TBXA2R):c.*715C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000185 in 1,531,294 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001060.6 3_prime_UTR
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBXA2R | NM_001060.6 | c.*715C>T | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000375190.10 | NP_001051.1 | ||
TBXA2R | NM_201636.3 | c.1087C>T | p.Arg363* | stop_gained | Exon 4 of 4 | NP_963998.2 | ||
TBXA2R | XM_011528214.3 | c.*715C>T | 3_prime_UTR_variant | Exon 4 of 4 | XP_011526516.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBXA2R | ENST00000375190 | c.*715C>T | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_001060.6 | ENSP00000364336.4 | |||
TBXA2R | ENST00000589966 | c.*578C>T | 3_prime_UTR_variant | Exon 2 of 2 | 1 | ENSP00000468145.1 | ||||
TBXA2R | ENST00000411851.3 | c.1087C>T | p.Arg363* | stop_gained | Exon 4 of 4 | 2 | ENSP00000393333.2 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 151974Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000114 AC: 16AN: 140504Hom.: 0 AF XY: 0.000106 AC XY: 8AN XY: 75692
GnomAD4 exome AF: 0.000194 AC: 267AN: 1379200Hom.: 0 Cov.: 29 AF XY: 0.000179 AC XY: 122AN XY: 680770
GnomAD4 genome AF: 0.000112 AC: 17AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74370
ClinVar
Submissions by phenotype
TBXA2R-related disorder Uncertain:1
The TBXA2R c.1087C>T variant is predicted to result in premature protein termination (p.Arg363*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.027% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Few loss-of-function variants have been reported in this gene to date in association with disease (Human Gene Mutation Database; https://www.hgmd.cf.ac.uk/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at