12-11061474-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_176887.2(TAS2R46):c.821C>T(p.Thr274Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000688 in 1,614,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_176887.2 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 |
---|---|---|---|---|---|---|---|
TAS2R46 | NM_176887.2 | c.821C>T | p.Thr274Ile | missense_variant | 1/1 | ENST00000533467.1 | |
PRH1-TAS2R14 | NM_001316893.2 | c.-133-14286C>T | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.205-14286C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R46 | ENST00000533467.1 | c.821C>T | p.Thr274Ile | missense_variant | 1/1 | NM_176887.2 | P1 | ||
TAS2R14 | ENST00000381852.4 | n.153-14286C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000541977.5 | n.124-14286C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000546265.1 | n.359-14286C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152236Hom.: 0 Cov.: 38
GnomAD3 exomes AF: 0.000128 AC: 32AN: 250234Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135700
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461778Hom.: 0 Cov.: 36 AF XY: 0.000102 AC XY: 74AN XY: 727188
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152354Hom.: 0 Cov.: 38 AF XY: 0.0000268 AC XY: 2AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.821C>T (p.T274I) alteration is located in exon 1 (coding exon 1) of the TAS2R46 gene. This alteration results from a C to T substitution at nucleotide position 821, causing the threonine (T) at amino acid position 274 to be replaced by an isoleucine (I). 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