rs41278022

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_138697.4(TAS1R1):c.1807C>T(p.Arg603Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00725 in 1,608,798 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R603H) has been classified as Benign.

Frequency

Genomes: 𝑓 0.0055 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0074 ( 59 hom. )

Consequence

TAS1R1
NM_138697.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.156

Publications

8 publications found

Variant links:

Genes affected

TAS1R1 (HGNC:14448): (taste 1 receptor member 1) The protein encoded by this gene is a G protein-coupled receptor and is a component of the heterodimeric amino acid taste receptor T1R1+3. The T1R1+3 receptor responds to L-amino acids but not to D-enantiomers or other compounds. Most amino acids that are perceived as sweet activate T1R1+3, and this activation is strictly dependent on an intact T1R1+3 heterodimer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]

TAS1R1 links:

LOC107984912 (HGNC:):

LOC107984912 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.013943106).

BP6

Variant 1-6578865-C-T is Benign according to our data. Variant chr1-6578865-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 767648.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R1	NM_138697.4 link	c.1807C>T	p.Arg603Cys	missense_variant	Exon 6 of 6	ENST00000333172.11	NP_619642.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
TAS1R1	ENST00000333172.11 link	c.1807C>T	p.Arg603Cys	missense_variant	Exon 6 of 6	1	NM_138697.4	ENSP00000331867.6
TAS1R1	ENST00000415267.1 link	c.608-431C>T		intron_variant	Intron 3 of 3	1		ENSP00000408448.1
TAS1R1	ENST00000351136.7 link	c.1045C>T	p.Arg349Cys	missense_variant	Exon 5 of 5	2		ENSP00000312558.5
TAS1R1	ENST00000411823.5 link	c.*30C>T		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000414166.1

Frequencies

GnomAD3 genomes

AF:

0.00553

AC:

841

AN:

152090

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00288

Gnomad ASJ

AF:

0.00605

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00754

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00935

Gnomad OTH

AF:

0.00239

GnomAD2 exomes

AF:

0.00611

AC:

1517

AN:

248086

AF XY:

0.00629

show subpopulations

Gnomad AFR exome

AF:

0.000990

Gnomad AMR exome

AF:

0.00196

Gnomad ASJ exome

AF:

0.00634

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00879

Gnomad NFE exome

AF:

0.00980

Gnomad OTH exome

AF:

0.00365

GnomAD4 exome

AF:

0.00743

AC:

10819

AN:

1456588

Hom.:

Cov.:

AF XY:

0.00748

AC XY:

5414

AN XY:

723740

show subpopulations

African (AFR)

AF:

0.000899

AC:

AN:

33380

American (AMR)

AF:

0.00227

AC:

101

AN:

44422

Ashkenazi Jewish (ASJ)

AF:

0.00676

AC:

175

AN:

25902

East Asian (EAS)

AF:

0.00

AC:

AN:

39584

South Asian (SAS)

AF:

0.00227

AC:

195

AN:

85886

European-Finnish (FIN)

AF:

0.00865

AC:

461

AN:

53304

Middle Eastern (MID)

AF:

0.00122

AC:

AN:

5738

European-Non Finnish (NFE)

AF:

0.00859

AC:

9518

AN:

1108268

Other (OTH)

AF:

0.00552

AC:

332

AN:

60104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

645

1291

1936

2582

3227

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

326

652

978

1304

1630

<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:

0.00553

AC:

841

AN:

152210

Hom.:

Cov.:

AF XY:

0.00481

AC XY:

358

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.00116

AC:

AN:

41500

American (AMR)

AF:

0.00288

AC:

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00605

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5170

South Asian (SAS)

AF:

0.00125

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.00754

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00935

AC:

636

AN:

68016

Other (OTH)

AF:

0.00236

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

133

178

222

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.00726

Hom.:

Bravo

AF:

0.00473

TwinsUK

AF:

0.00809

AC:

ALSPAC

AF:

0.00856

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00698

AC:

ExAC

AF:

0.00621

AC:

754

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00834

EpiControl

AF:

0.00724

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jun 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

TAS1R1: BS2 -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

May 18, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.23

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.43

T;.

Eigen

Benign

-0.43

Eigen_PC

Benign

-0.63

FATHMM_MKL

Benign

0.10

LIST_S2

Uncertain

0.90

D;D

M_CAP

Benign

0.079

MetaRNN

Benign

0.014

T;T

MetaSVM

Benign

-0.38

MutationAssessor

Uncertain

2.1

M;.

PhyloP100

0.16

PrimateAI

Benign

0.37

PROVEAN

Uncertain

-3.9

D;D

REVEL

Uncertain

0.32

Sift

Uncertain

0.010

D;D

Sift4G

Uncertain

0.0090

D;D

Polyphen

1.0

D;D

Vest4

0.42

MVP

0.62

MPC

0.78

ClinPred

0.040

GERP RS

-2.5

Varity_R

0.44

gMVP

0.34

Mutation Taster

=95/5

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over