chr12-11061788-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_176887.2(TAS2R46):c.507G>T(p.Arg169Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000151 in 1,614,128 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.507G>T | p.Arg169Ser | missense_variant | 1/1 | ENST00000533467.1 | |
PRH1-TAS2R14 | NM_001316893.2 | c.-133-14600G>T | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.205-14600G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R46 | ENST00000533467.1 | c.507G>T | p.Arg169Ser | missense_variant | 1/1 | NM_176887.2 | P1 | ||
TAS2R14 | ENST00000381852.4 | n.153-14600G>T | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000541977.5 | n.124-14600G>T | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000546265.1 | n.359-14600G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152238Hom.: 0 Cov.: 39
GnomAD3 exomes AF: 0.000172 AC: 43AN: 250004Hom.: 1 AF XY: 0.000177 AC XY: 24AN XY: 135446
GnomAD4 exome AF: 0.000146 AC: 214AN: 1461772Hom.: 0 Cov.: 83 AF XY: 0.000144 AC XY: 105AN XY: 727176
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152356Hom.: 0 Cov.: 39 AF XY: 0.000201 AC XY: 15AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 11, 2021 | The c.507G>T (p.R169S) alteration is located in exon 1 (coding exon 1) of the TAS2R46 gene. This alteration results from a G to T substitution at nucleotide position 507, causing the arginine (R) at amino acid position 169 to be replaced by a serine (S). 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