1-1331815-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_152228.3(TAS1R3):c.369C>T(p.Arg123Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,612,738 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 Likely benign (★).
Frequency
Consequence
NM_152228.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAS1R3 | NM_152228.3 | c.369C>T | p.Arg123Arg | synonymous_variant | Exon 2 of 6 | ENST00000339381.6 | NP_689414.2 | |
TAS1R3 | XM_017002435.2 | c.369C>T | p.Arg123Arg | synonymous_variant | Exon 2 of 5 | XP_016857924.1 | ||
TAS1R3 | XM_017002436.2 | c.369C>T | p.Arg123Arg | synonymous_variant | Exon 2 of 5 | XP_016857925.1 | ||
TAS1R3 | XM_047431571.1 | c.369C>T | p.Arg123Arg | synonymous_variant | Exon 2 of 6 | XP_047287527.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249534Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135502
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1460508Hom.: 0 Cov.: 31 AF XY: 0.0000358 AC XY: 26AN XY: 726544
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152230Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at