rs5763
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001061.7(TBXAS1):c.1349C>A(p.Thr450Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 1,613,866 control chromosomes in the GnomAD database, including 337 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001061.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBXAS1 | NM_001061.7 | c.1349C>A | p.Thr450Asn | missense_variant | 11/13 | ENST00000448866.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBXAS1 | ENST00000448866.7 | c.1349C>A | p.Thr450Asn | missense_variant | 11/13 | 1 | NM_001061.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0141 AC: 2146AN: 152182Hom.: 22 Cov.: 33
GnomAD3 exomes AF: 0.0141 AC: 3529AN: 250862Hom.: 38 AF XY: 0.0145 AC XY: 1964AN XY: 135676
GnomAD4 exome AF: 0.0193 AC: 28250AN: 1461566Hom.: 315 Cov.: 32 AF XY: 0.0191 AC XY: 13903AN XY: 727120
GnomAD4 genome ? AF: 0.0141 AC: 2147AN: 152300Hom.: 22 Cov.: 33 AF XY: 0.0133 AC XY: 991AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 03, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at