Variant chr12-10938833-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_023922.2(TAS2R14):c.375G>A(p.Arg125=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 1,613,234 control chromosomes in the GnomAD database, including 564,470 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 0.77 ( 46280 hom., cov: 32)

Exomes 𝑓: 0.84 ( 518190 hom. )

Consequence

TAS2R14
NM_023922.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.297

Variant links:

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]

TAS2R14 links:

PRH1-TAS2R14 (HGNC:):

PRH1-TAS2R14 links:

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]

PRH1 links:

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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=-0.77).

BP7

Synonymous conserved (PhyloP=0.297 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
TAS2R14	NM_023922.2 linkuse as main transcript	c.375G>A	p.Arg125=	synonymous_variant	1/1	ENST00000537503.2	NP_076411.1
PRH1-TAS2R14	NM_001316893.2 linkuse as main transcript	c.208-256G>A		intron_variant			NP_001303822.1
PRH1-PRR4	NR_037918.2 linkuse as main transcript	n.544+34822G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS2R14	ENST00000537503.2 linkuse as main transcript	c.375G>A	p.Arg125=	synonymous_variant	1/1		NM_023922.2	ENSP00000441949	P1
	ENST00000703543.1 linkuse as main transcript	c.-59+34822G>A		intron_variant				ENSP00000515364	P1

Frequencies

GnomAD3 genomes

AF:

0.767

AC:

116542

AN:

151966

Hom.:

46268

Cov.:

show subpopulations

Gnomad AFR

AF:

0.536

Gnomad AMI

AF:

0.861

Gnomad AMR

AF:

0.831

Gnomad ASJ

AF:

0.845

Gnomad EAS

AF:

0.936

Gnomad SAS

AF:

0.859

Gnomad FIN

AF:

0.924

Gnomad MID

AF:

0.854

Gnomad NFE

AF:

0.843

Gnomad OTH

AF:

0.781

GnomAD3 exomes

AF:

0.849

AC:

212389

AN:

250028

Hom.:

91187

AF XY:

0.854

AC XY:

115508

AN XY:

135260

show subpopulations

Gnomad AFR exome

AF:

0.533

Gnomad AMR exome

AF:

0.890

Gnomad ASJ exome

AF:

0.844

Gnomad EAS exome

AF:

0.937

Gnomad SAS exome

AF:

0.874

Gnomad FIN exome

AF:

0.923

Gnomad NFE exome

AF:

0.848

Gnomad OTH exome

AF:

0.845

GnomAD4 exome

AF:

0.840

AC:

1227716

AN:

1461150

Hom.:

518190

Cov.:

AF XY:

0.842

AC XY:

611973

AN XY:

726872

show subpopulations

Gnomad4 AFR exome

AF:

0.534

Gnomad4 AMR exome

AF:

0.887

Gnomad4 ASJ exome

AF:

0.848

Gnomad4 EAS exome

AF:

0.955

Gnomad4 SAS exome

AF:

0.864

Gnomad4 FIN exome

AF:

0.920

Gnomad4 NFE exome

AF:

0.838

Gnomad4 OTH exome

AF:

0.833

GnomAD4 genome

AF:

0.767

AC:

116580

AN:

152084

Hom.:

46280

Cov.:

AF XY:

0.775

AC XY:

57592

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.535

Gnomad4 AMR

AF:

0.831

Gnomad4 ASJ

AF:

0.845

Gnomad4 EAS

AF:

0.936

Gnomad4 SAS

AF:

0.859

Gnomad4 FIN

AF:

0.924

Gnomad4 NFE

AF:

0.843

Gnomad4 OTH

AF:

0.783

Alfa

AF:

0.835

Hom.:

66727

Bravo

AF:

0.751

Asia WGS

AF:

0.893

AC:

3102

AN:

3478

EpiCase

AF:

0.843

EpiControl

AF:

0.841

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

2.4

DANN

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over