rs1868769
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_176888.2(TAS2R19):c.418C>T(p.Leu140=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 1,612,746 control chromosomes in the GnomAD database, including 499,872 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.71 ( 39761 hom., cov: 33)
Exomes 𝑓: 0.79 ( 460111 hom. )
Consequence
TAS2R19
NM_176888.2 synonymous
NM_176888.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.137
Genes affected
TAS2R19 (HGNC:19108): (taste 2 receptor member 19) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway and sensory perception of taste. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
PRH1 (HGNC:9366): (proline rich protein HaeIII subfamily 1) This gene encodes a member of the heterogeneous family of proline-rich salivary glycoproteins. The encoded preproprotein undergoes proteolytic processing to generate one or more mature isoforms before secretion from the parotid and submandibular/sublingual glands. Multiple distinct alleles of this locus including the parotid isoelectric-focusing variant slow (PIF-s), the parotid acidic protein (Pa), and the double band slow (Db-s) isoforms have been characterized. The reference genome encodes the Db-s allele. Certain alleles of this gene are associated with susceptibility to dental caries. This gene is located in a cluster of closely related salivary proline-rich proteins on chromosome 12. Co-transcription of this gene with adjacent genes has been observed. Alternate splicing of this gene results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Oct 2015]
TAS2R14 (HGNC:14920): (taste 2 receptor member 14) This gene product belongs to the family of candidate taste receptors that are members of the G-protein-coupled receptor superfamily. These proteins are specifically expressed in the taste receptor cells of the tongue and palate epithelia. They are organized in the genome in clusters and are genetically linked to loci that influence bitter perception in mice and humans. In functional expression studies, they respond to bitter tastants. This gene maps to the taste receptor gene cluster on chromosome 12p13. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.03).
BP7
?
Synonymous conserved (PhyloP=0.137 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS2R19 | NM_176888.2 | c.418C>T | p.Leu140= | synonymous_variant | 1/1 | ENST00000390673.2 | |
PRH1-TAS2R14 | NM_001316893.2 | c.140+12628C>T | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.477+12628C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R19 | ENST00000390673.2 | c.418C>T | p.Leu140= | synonymous_variant | 1/1 | NM_176888.2 | P1 | ||
ENST00000703543.1 | c.-126+24866C>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.709 AC: 107208AN: 151182Hom.: 39747 Cov.: 33
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GnomAD3 exomes AF: 0.788 AC: 198111AN: 251252Hom.: 79398 AF XY: 0.790 AC XY: 107294AN XY: 135802
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GnomAD4 exome AF: 0.791 AC: 1155826AN: 1461438Hom.: 460111 Cov.: 55 AF XY: 0.790 AC XY: 574493AN XY: 727008
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GnomAD4 genome ? AF: 0.709 AC: 107243AN: 151308Hom.: 39761 Cov.: 33 AF XY: 0.714 AC XY: 52841AN XY: 73980
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at