rs7138535
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_023922.2(TAS2R14):c.114A>T(p.Gly38=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,613,454 control chromosomes in the GnomAD database, including 49,909 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 0.24 ( 4418 hom., cov: 32)
Exomes 𝑓: 0.25 ( 45491 hom. )
Consequence
TAS2R14
NM_023922.2 synonymous
NM_023922.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.08
Genes affected
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]
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]
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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=-0.91).
BP7
?
Synonymous conserved (PhyloP=-1.09 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS2R14 | NM_023922.2 | c.114A>T | p.Gly38= | synonymous_variant | 1/1 | ENST00000537503.2 | |
PRH1-TAS2R14 | NM_001316893.2 | c.208-517A>T | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.544+34561A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R14 | ENST00000537503.2 | c.114A>T | p.Gly38= | synonymous_variant | 1/1 | NM_023922.2 | P1 | ||
ENST00000703543.1 | c.-59+34561A>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.238 AC: 36215AN: 151988Hom.: 4415 Cov.: 32
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GnomAD3 exomes AF: 0.243 AC: 60870AN: 250642Hom.: 7638 AF XY: 0.238 AC XY: 32271AN XY: 135542
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GnomAD4 exome AF: 0.248 AC: 361990AN: 1461348Hom.: 45491 Cov.: 35 AF XY: 0.245 AC XY: 178369AN XY: 726958
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GnomAD4 genome ? AF: 0.238 AC: 36229AN: 152106Hom.: 4418 Cov.: 32 AF XY: 0.239 AC XY: 17777AN XY: 74352
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ClinVar
Not reported inComputational scores
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Name
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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