chr1-1332115-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152228.3(TAS1R3):c.584C>T(p.Thr195Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000662 in 1,599,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152228.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS1R3 | NM_152228.3 | c.584C>T | p.Thr195Met | missense_variant | 3/6 | ENST00000339381.6 | |
TAS1R3 | XM_017002435.2 | c.584C>T | p.Thr195Met | missense_variant | 3/5 | ||
TAS1R3 | XM_017002436.2 | c.584C>T | p.Thr195Met | missense_variant | 3/5 | ||
TAS1R3 | XM_047431571.1 | c.584C>T | p.Thr195Met | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS1R3 | ENST00000339381.6 | c.584C>T | p.Thr195Met | missense_variant | 3/6 | 2 | NM_152228.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000506 AC: 77AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000314 AC: 72AN: 229332Hom.: 0 AF XY: 0.000291 AC XY: 37AN XY: 127176
GnomAD4 exome AF: 0.000678 AC: 982AN: 1447460Hom.: 0 Cov.: 75 AF XY: 0.000677 AC XY: 488AN XY: 720626
GnomAD4 genome AF: 0.000505 AC: 77AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.584C>T (p.T195M) alteration is located in exon 3 (coding exon 3) of the TAS1R3 gene. This alteration results from a C to T substitution at nucleotide position 584, causing the threonine (T) at amino acid position 195 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at