chr12-11092131-A-G
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_176884.2(TAS2R43):āc.99T>Cā(p.Ile33=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 794,654 control chromosomes in the GnomAD database, including 101,404 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.38 ( 3220 hom., cov: 22)
Exomes š: 0.46 ( 98184 hom. )
Consequence
TAS2R43
NM_176884.2 synonymous
NM_176884.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.923
Genes affected
TAS2R43 (HGNC:18875): (taste 2 receptor member 43) TAS2R43 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, Mar 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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 12-11092131-A-G is Benign according to our data. Variant chr12-11092131-A-G is described in ClinVar as [Benign]. Clinvar id is 768524.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.923 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
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TAS2R43 | NM_176884.2 | c.99T>C | p.Ile33= | synonymous_variant | 1/1 | ENST00000531678.1 | |
PRH1-TAS2R14 | NM_001316893.2 | c.-133-44943T>C | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.205-44943T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R43 | ENST00000531678.1 | c.99T>C | p.Ile33= | synonymous_variant | 1/1 | NM_176884.2 | P1 | ||
TAS2R14 | ENST00000381852.4 | n.153-44943T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000541977.5 | n.124-44943T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
PRH1 | ENST00000546265.1 | n.358+28879T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.383 AC: 31829AN: 83030Hom.: 3219 Cov.: 22
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GnomAD3 exomes AF: 0.00106 AC: 208AN: 196882Hom.: 75 AF XY: 0.000880 AC XY: 95AN XY: 107894
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GnomAD4 exome AF: 0.459 AC: 326675AN: 711506Hom.: 98184 Cov.: 48 AF XY: 0.462 AC XY: 163941AN XY: 354798
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GnomAD4 genome AF: 0.383 AC: 31838AN: 83148Hom.: 3220 Cov.: 22 AF XY: 0.387 AC XY: 15638AN XY: 40454
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 25, 2017 | - - |
Computational scores
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DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at