Variant chr12-10939094-T-A 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.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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

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=-0.91).

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	Protein
TAS2R14	NM_023922.2 linkuse as main transcript	c.114A>T	p.Gly38=	synonymous_variant	1/1	ENST00000537503.2	NP_076411.1
PRH1-TAS2R14	NM_001316893.2 linkuse as main transcript	c.208-517A>T		intron_variant			NP_001303822.1
PRH1-PRR4	NR_037918.2 linkuse as main transcript	n.544+34561A>T		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.114A>T	p.Gly38=	synonymous_variant	1/1		NM_023922.2	ENSP00000441949	P1
	ENST00000703543.1 linkuse as main transcript	c.-59+34561A>T		intron_variant				ENSP00000515364	P1

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

36215

AN:

151988

Hom.:

4415

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.255

Gnomad ASJ

AF:

0.171

Gnomad EAS

AF:

0.230

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.274

Gnomad MID

AF:

0.179

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.228

GnomAD3 exomes

AF:

0.243

AC:

60870

AN:

250642

Hom.:

7638

AF XY:

0.238

AC XY:

32271

AN XY:

135542

show subpopulations

Gnomad AFR exome

AF:

0.222

Gnomad AMR exome

AF:

0.303

Gnomad ASJ exome

AF:

0.173

Gnomad EAS exome

AF:

0.218

Gnomad SAS exome

AF:

0.184

Gnomad FIN exome

AF:

0.271

Gnomad NFE exome

AF:

0.249

Gnomad OTH exome

AF:

0.227

GnomAD4 exome

AF:

0.248

AC:

361990

AN:

1461348

Hom.:

45491

Cov.:

AF XY:

0.245

AC XY:

178369

AN XY:

726958

show subpopulations

Gnomad4 AFR exome

AF:

0.219

Gnomad4 AMR exome

AF:

0.297

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.231

Gnomad4 SAS exome

AF:

0.184

Gnomad4 FIN exome

AF:

0.276

Gnomad4 NFE exome

AF:

0.253

Gnomad4 OTH exome

AF:

0.238

GnomAD4 genome

AF:

0.238

AC:

36229

AN:

152106

Hom.:

4418

Cov.:

AF XY:

0.239

AC XY:

17777

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.214

Gnomad4 AMR

AF:

0.255

Gnomad4 ASJ

AF:

0.171

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.186

Gnomad4 FIN

AF:

0.274

Gnomad4 NFE

AF:

0.254

Gnomad4 OTH

AF:

0.226

Alfa

AF:

0.242

Hom.:

1505

Bravo

AF:

0.235

Asia WGS

AF:

0.235

AC:

818

AN:

3478

EpiCase

AF:

0.238

EpiControl

AF:

0.240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.1

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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