Variant chr1-6575171-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000333172.11(TAS1R1):c.1039A>G(p.Lys347Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 1,595,622 control chromosomes in the GnomAD database, including 779,265 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.93 ( 66755 hom., cov: 36)

Exomes 𝑓: 0.99 ( 712510 hom. )

Consequence

TAS1R1
ENST00000333172.11 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.130

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.1004017E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS1R1	NM_138697.4 linkuse as main transcript	c.1039A>G	p.Lys347Glu	missense_variant	3/6	ENST00000333172.11	NP_619642.2
LOC107984912	XR_002958250.1 linkuse as main transcript	n.87+4176T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS1R1	ENST00000333172.11 linkuse as main transcript	c.1039A>G	p.Lys347Glu	missense_variant	3/6	1	NM_138697.4	ENSP00000331867	P1	Q7RTX1-1
TAS1R1	ENST00000415267.1 linkuse as main transcript	c.276-1244A>G		intron_variant		1		ENSP00000408448
TAS1R1	ENST00000411823.5 linkuse as main transcript	c.817A>G	p.Lys273Glu	missense_variant	2/3	2		ENSP00000414166
TAS1R1	ENST00000351136.7 linkuse as main transcript	c.499-1244A>G		intron_variant		2		ENSP00000312558		Q7RTX1-2

Frequencies

GnomAD3 genomes

AF:

0.930

AC:

141583

AN:

152234

Hom.:

66718

Cov.:

show subpopulations

Gnomad AFR

AF:

0.756

Gnomad AMI

AF:

0.996

Gnomad AMR

AF:

0.975

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.999

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.987

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.950

GnomAD3 exomes

AF:

0.981

AC:

229137

AN:

233682

Hom.:

112813

AF XY:

0.986

AC XY:

124927

AN XY:

126732

show subpopulations

Gnomad AFR exome

AF:

0.750

Gnomad AMR exome

AF:

0.988

Gnomad ASJ exome

AF:

0.999

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.999

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

0.999

Gnomad OTH exome

AF:

0.990

GnomAD4 exome

AF:

0.993

AC:

1433087

AN:

1443270

Hom.:

712510

Cov.:

AF XY:

0.994

AC XY:

713470

AN XY:

717832

show subpopulations

Gnomad4 AFR exome

AF:

0.754

Gnomad4 AMR exome

AF:

0.986

Gnomad4 ASJ exome

AF:

0.999

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.999

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.984

GnomAD4 genome

AF:

0.930

AC:

141675

AN:

152352

Hom.:

66755

Cov.:

AF XY:

0.932

AC XY:

69445

AN XY:

74498

show subpopulations

Gnomad4 AFR

AF:

0.756

Gnomad4 AMR

AF:

0.975

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.999

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.951

Alfa

AF:

0.986

Hom.:

107164

Bravo

AF:

0.920

TwinsUK

AF:

0.999

AC:

3706

ALSPAC

AF:

0.999

AC:

3852

ESP6500AA

AF:

0.764

AC:

3368

ESP6500EA

AF:

0.999

AC:

8594

ExAC

AF:

0.977

AC:

118579

Asia WGS

AF:

0.985

AC:

3427

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.067

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.38

CADD

Benign

2.0

DANN

Benign

0.34

DEOGEN2

Benign

0.058

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.0057

LIST_S2

Benign

0.059

MetaRNN

Benign

0.0000011

MetaSVM

Benign

-0.97

MutationAssessor

Benign

-1.4

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.13

REVEL

Benign

0.22

Sift

Benign

0.99

Sift4G

Benign

0.74

Polyphen

0.017

Vest4

0.031

MPC

0.23

ClinPred

0.0089

GERP RS

-0.46

Varity_R

0.078

gMVP

0.31

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