12-10938833-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_023922.2(TAS2R14):c.375G>A(p.Arg125Arg) 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

Publications

37 publications found

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:

ENSG00000275778 (HGNC:):

ENSG00000275778 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:

PRR4 (HGNC:18020): (proline rich 4) This gene encodes a member of the proline-rich protein family that lacks a conserved repetitive domain. This protein may play a role in protective functions in the eye. Alternative splicing result in multiple transcript variants. Read-through transcription also exists between this gene and the upstream PRH1 (proline-rich protein HaeIII subfamily 1) gene. [provided by RefSeq, Feb 2011]

PRR4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_023922.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TAS2R14	NM_023922.2	MANE Select	c.375G>A	p.Arg125Arg	synonymous	Exon 1 of 1	NP_076411.1	Q9NYV8
PRH1	NM_001291315.2		c.103+34822G>A		intron	N/A	NP_001278244.1
PRH1	NM_001291314.2		c.-59+34822G>A		intron	N/A	NP_001278243.1	A0A087WV42

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TAS2R14	ENST00000537503.2	TSL:6 MANE Select	c.375G>A	p.Arg125Arg	synonymous	Exon 1 of 1	ENSP00000441949.1	Q9NYV8
ENSG00000275778	ENST00000536668.2	TSL:5	n.176+34822G>A		intron	N/A	ENSP00000482961.1	A0A087WZY1
PRH1	ENST00000703543.1		c.-59+34822G>A		intron	N/A	ENSP00000515364.1	A0A087WYT0

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

GnomAD2 exomes

AF:

0.849

AC:

212389

AN:

250028

AF XY:

0.854

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 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

African (AFR)

AF:

0.534

AC:

17859

AN:

33444

American (AMR)

AF:

0.887

AC:

39589

AN:

44648

Ashkenazi Jewish (ASJ)

AF:

0.848

AC:

22144

AN:

26122

East Asian (EAS)

AF:

0.955

AC:

37915

AN:

39692

South Asian (SAS)

AF:

0.864

AC:

74454

AN:

86190

European-Finnish (FIN)

AF:

0.920

AC:

48821

AN:

53084

Middle Eastern (MID)

AF:

0.857

AC:

4944

AN:

5766

European-Non Finnish (NFE)

AF:

0.838

AC:

931697

AN:

1111826

Other (OTH)

AF:

0.833

AC:

50293

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

11190

22380

33571

44761

55951

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21042

42084

63126

84168

105210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.767

AC:

116580

AN:

152084

Hom.:

46280

Cov.:

AF XY:

0.775

AC XY:

57592

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.535

AC:

22179

AN:

41436

American (AMR)

AF:

0.831

AC:

12700

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.845

AC:

2934

AN:

3472

East Asian (EAS)

AF:

0.936

AC:

4843

AN:

5176

South Asian (SAS)

AF:

0.859

AC:

4147

AN:

4826

European-Finnish (FIN)

AF:

0.924

AC:

9796

AN:

10600

Middle Eastern (MID)

AF:

0.850

AC:

250

AN:

294

European-Non Finnish (NFE)

AF:

0.843

AC:

57296

AN:

67986

Other (OTH)

AF:

0.783

AC:

1650

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1221

2442

3664

4885

6106

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.824

Hom.:

83650

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

2.4

(source)

DANN

Benign

0.79

PhyloP100

0.30

PromoterAI

-0.0049

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over