chr12-11061613-A-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_176887.2(TAS2R46):c.682T>A(p.Leu228Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 1,599,916 control chromosomes in the GnomAD database, including 173,657 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_176887.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS2R46 | NM_176887.2 | c.682T>A | p.Leu228Met | missense_variant | 1/1 | ENST00000533467.1 | |
PRH1-TAS2R14 | NM_001316893.2 | c.-133-14425T>A | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.205-14425T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R46 | ENST00000533467.1 | c.682T>A | p.Leu228Met | missense_variant | 1/1 | NM_176887.2 | P1 | ||
TAS2R14 | ENST00000381852.4 | n.153-14425T>A | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000541977.5 | n.124-14425T>A | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000546265.1 | n.359-14425T>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.378 AC: 55845AN: 147564Hom.: 6720 Cov.: 34
GnomAD3 exomes AF: 0.429 AC: 107807AN: 251256Hom.: 24929 AF XY: 0.421 AC XY: 57231AN XY: 135810
GnomAD4 exome AF: 0.473 AC: 687408AN: 1452230Hom.: 166939 Cov.: 92 AF XY: 0.466 AC XY: 336896AN XY: 722636
GnomAD4 genome AF: 0.378 AC: 55859AN: 147686Hom.: 6718 Cov.: 34 AF XY: 0.377 AC XY: 27193AN XY: 72152
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at