12-11062283-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_176887.2(TAS2R46):c.12T>G(p.Phe4Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,611,578 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_176887.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS2R46 | NM_176887.2 | c.12T>G | p.Phe4Leu | missense_variant | 1/1 | ENST00000533467.1 | |
PRH1-TAS2R14 | NM_001316893.2 | c.-133-15095T>G | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.205-15095T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R46 | ENST00000533467.1 | c.12T>G | p.Phe4Leu | missense_variant | 1/1 | NM_176887.2 | P1 | ||
TAS2R14 | ENST00000381852.4 | n.153-15095T>G | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000541977.5 | n.124-15095T>G | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000546265.1 | n.359-15095T>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000572 AC: 14AN: 244886Hom.: 0 AF XY: 0.0000526 AC XY: 7AN XY: 132960
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1459296Hom.: 0 Cov.: 37 AF XY: 0.0000262 AC XY: 19AN XY: 725844
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74464
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 21, 2024 | 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