Genetic Variant NM_019599.3:c.850T>C (chr5-9629183-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_019599.3(TAS2R1):c.850T>C(p.Leu284Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0327 in 1,590,698 control chromosomes in the GnomAD database, including 944 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 0.028 ( 74 hom., cov: 32)

Exomes 𝑓: 0.033 ( 870 hom. )

Consequence

TAS2R1
NM_019599.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147

Publications

8 publications found

Variant links:

Genes affected

TAS2R1 (HGNC:14909): (taste 2 receptor member 1) This gene encodes a member of a family of candidate taste receptors that are members of the G protein-coupled receptor superfamily and that are specifically expressed by taste receptor cells of the tongue and palate epithelia. This intronless taste receptor gene encodes a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is mapped to chromosome 5p15, the location of a genetic locus (PROP) that controls the detection of the bitter compound 6-n-propyl-2-thiouracil. [provided by RefSeq, Jul 2008]

TAS2R1 links:

ENSG00000248525 (HGNC:):

ENSG00000248525 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=-0.56).

BP7

Synonymous conserved (PhyloP=0.147 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R1	NM_019599.3 link	c.850T>C	p.Leu284Leu	synonymous_variant	Exon 1 of 1	ENST00000382492.4	NP_062545.1	Q9NYW7Q502V6
TAS2R1	NM_001386348.1 link	c.730T>C	p.Leu244Leu	synonymous_variant	Exon 10 of 10		NP_001373277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R1	ENST00000382492.4 link	c.850T>C	p.Leu284Leu	synonymous_variant	Exon 1 of 1	6	NM_019599.3	ENSP00000371932.2		Q9NYW7
ENSG00000248525	ENST00000504182.2 link	n.36-5581T>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.0282

AC:

4288

AN:

152170

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0207

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.0234

Gnomad ASJ

AF:

0.0522

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0364

Gnomad FIN

AF:

0.0267

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0340

Gnomad OTH

AF:

0.0311

GnomAD2 exomes

AF:

0.0312

AC:

7193

AN:

230806

AF XY:

0.0326

show subpopulations

Gnomad AFR exome

AF:

0.0212

Gnomad AMR exome

AF:

0.0204

Gnomad ASJ exome

AF:

0.0570

Gnomad EAS exome

AF:

0.000175

Gnomad FIN exome

AF:

0.0279

Gnomad NFE exome

AF:

0.0368

Gnomad OTH exome

AF:

0.0348

GnomAD4 exome

AF:

0.0332

AC:

47694

AN:

1438410

Hom.:

870

Cov.:

AF XY:

0.0335

AC XY:

23932

AN XY:

714904

show subpopulations

African (AFR)

AF:

0.0198

AC:

630

AN:

31854

American (AMR)

AF:

0.0197

AC:

750

AN:

38036

Ashkenazi Jewish (ASJ)

AF:

0.0513

AC:

1261

AN:

24578

East Asian (EAS)

AF:

0.000152

AC:

AN:

39506

South Asian (SAS)

AF:

0.0378

AC:

3147

AN:

83298

European-Finnish (FIN)

AF:

0.0295

AC:

1558

AN:

52840

Middle Eastern (MID)

AF:

0.0637

AC:

357

AN:

5606

European-Non Finnish (NFE)

AF:

0.0344

AC:

37966

AN:

1103536

Other (OTH)

AF:

0.0341

AC:

2019

AN:

59156

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

2456

4912

7368

9824

12280

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1452

2904

4356

5808

7260

<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:

0.0282

AC:

4294

AN:

152288

Hom.:

Cov.:

AF XY:

0.0282

AC XY:

2098

AN XY:

74478

show subpopulations

African (AFR)

AF:

0.0208

AC:

863

AN:

41550

American (AMR)

AF:

0.0235

AC:

359

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0522

AC:

181

AN:

3468

East Asian (EAS)

AF:

0.000578

AC:

AN:

5186

South Asian (SAS)

AF:

0.0364

AC:

176

AN:

4830

European-Finnish (FIN)

AF:

0.0267

AC:

283

AN:

10618

Middle Eastern (MID)

AF:

0.0782

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0340

AC:

2310

AN:

68028

Other (OTH)

AF:

0.0312

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

225

450

674

899

1124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<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:

0.0329

Hom.:

246

Bravo

AF:

0.0276

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

0.15

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over