12-10939193-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_023922.2(TAS2R14):c.15A>G(p.Ile5Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000582 in 1,573,182 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0032 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00030 ( 2 hom. )
Consequence
TAS2R14
NM_023922.2 missense
NM_023922.2 missense
Scores
2
15
Clinical Significance
Conservation
PhyloP100: -0.974
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0037686527).
BP6
?
Variant 12-10939193-T-C is Benign according to our data. Variant chr12-10939193-T-C is described in ClinVar as [Benign]. Clinvar id is 717257.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS2R14 | NM_023922.2 | c.15A>G | p.Ile5Met | missense_variant | 1/1 | ENST00000537503.2 | |
PRH1-TAS2R14 | NM_001316893.2 | c.208-616A>G | intron_variant | ||||
PRH1-PRR4 | NR_037918.2 | n.544+34462A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS2R14 | ENST00000537503.2 | c.15A>G | p.Ile5Met | missense_variant | 1/1 | NM_023922.2 | P1 | ||
ENST00000703543.1 | c.-59+34462A>G | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00319 AC: 485AN: 152228Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.000978 AC: 204AN: 208516Hom.: 0 AF XY: 0.000678 AC XY: 76AN XY: 112012
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GnomAD4 exome AF: 0.000301 AC: 427AN: 1420836Hom.: 2 Cov.: 30 AF XY: 0.000260 AC XY: 183AN XY: 704132
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GnomAD4 genome ? AF: 0.00321 AC: 489AN: 152346Hom.: 3 Cov.: 32 AF XY: 0.00336 AC XY: 250AN XY: 74504
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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 | Apr 24, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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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