12-11062211-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_176887.2(TAS2R46):c.84A>G(p.Ala28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000074 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000022 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TAS2R46
NM_176887.2 synonymous
NM_176887.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.86
Genes affected
TAS2R46 (HGNC:18877): (taste 2 receptor member 46) TAS2R46 belongs to the large TAS2R receptor family. TAS2Rs are expressed on the surface of taste receptor cells and mediate the perception of bitterness through a G protein-coupled second messenger pathway (Conte et al., 2002 [PubMed 12584440]). For further information on TAS2Rs, see MIM 604791.[supplied by OMIM, Sep 2009]
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 -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 12-11062211-T-C is Benign according to our data. Variant chr12-11062211-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2642703.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.86 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS2R46 | NM_176887.2 | c.84A>G | p.Ala28= | synonymous_variant | 1/1 | ENST00000533467.1 | |
PRH1-TAS2R14 | NM_001316893.2 | c.-133-15023A>G | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.205-15023A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R46 | ENST00000533467.1 | c.84A>G | p.Ala28= | synonymous_variant | 1/1 | NM_176887.2 | P1 | ||
TAS2R14 | ENST00000381852.4 | n.153-15023A>G | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000541977.5 | n.124-15023A>G | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000546265.1 | n.359-15023A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 11AN: 148956Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000221 AC: 32AN: 1448596Hom.: 0 Cov.: 38 AF XY: 0.0000236 AC XY: 17AN XY: 720732
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000738 AC: 11AN: 149078Hom.: 0 Cov.: 32 AF XY: 0.000124 AC XY: 9AN XY: 72862
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | TAS2R46: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at