Genetic Variant TAS1R3:c.*485A>G (chr1-1334949-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152228.3(TAS1R3):c.*485A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 156,970 control chromosomes in the GnomAD database, including 73,948 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 0.97 ( 71763 hom., cov: 36)

Exomes 𝑓: 0.97 ( 2185 hom. )

Consequence

TAS1R3
NM_152228.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.282

Publications

1 publications found

Variant links:

Genes affected

TAS1R3 (HGNC:15661): (taste 1 receptor member 3) The protein encoded by this gene is a G-protein coupled receptor involved in taste responses. The encoded protein can form a heterodimeric receptor with TAS1R1 to elicit the umami taste response, or it can bind with TAS1R2 to form a receptor for the sweet taste response. [provided by RefSeq, Nov 2015]

TAS1R3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
TAS1R3	NM_152228.3 link	c.*485A>G	3_prime_UTR_variant	Exon 6 of 6	ENST00000339381.6	NP_689414.2	Q7RTX0
TAS1R3	XM_017002435.2 link	c.*485A>G	3_prime_UTR_variant	Exon 5 of 5		XP_016857924.1
TAS1R3	XM_017002436.2 link	c.*485A>G	3_prime_UTR_variant	Exon 5 of 5		XP_016857925.1
TAS1R3	XM_047431571.1 link	c.*485A>G	3_prime_UTR_variant	Exon 6 of 6		XP_047287527.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R3	ENST00000339381.6 link	c.*485A>G		3_prime_UTR_variant	Exon 6 of 6	2	NM_152228.3	ENSP00000344411.5		Q7RTX0

Frequencies

GnomAD3 genomes

AF:

0.970

AC:

147699

AN:

152208

Hom.:

71707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.988

Gnomad AMI

AF:

0.959

Gnomad AMR

AF:

0.980

Gnomad ASJ

AF:

0.977

Gnomad EAS

AF:

0.907

Gnomad SAS

AF:

0.915

Gnomad FIN

AF:

0.923

Gnomad MID

AF:

0.949

Gnomad NFE

AF:

0.974

Gnomad OTH

AF:

0.967

GnomAD4 exome

AF:

0.970

AC:

4503

AN:

4644

Hom.:

2185

Cov.:

AF XY:

0.967

AC XY:

2283

AN XY:

2360

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.977

AC:

719

AN:

736

Ashkenazi Jewish (ASJ)

AF:

0.987

AC:

AN:

East Asian (EAS)

AF:

0.971

AC:

AN:

South Asian (SAS)

AF:

0.888

AC:

229

AN:

258

European-Finnish (FIN)

AF:

0.907

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.975

AC:

3047

AN:

3126

Other (OTH)

AF:

0.977

AC:

213

AN:

218

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

160

<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:

0.970

AC:

147815

AN:

152326

Hom.:

71763

Cov.:

AF XY:

0.967

AC XY:

72042

AN XY:

74478

show subpopulations

African (AFR)

AF:

0.988

AC:

41083

AN:

41578

American (AMR)

AF:

0.980

AC:

14999

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.977

AC:

3392

AN:

3472

East Asian (EAS)

AF:

0.907

AC:

4690

AN:

5170

South Asian (SAS)

AF:

0.914

AC:

4417

AN:

4830

European-Finnish (FIN)

AF:

0.923

AC:

9808

AN:

10622

Middle Eastern (MID)

AF:

0.946

AC:

278

AN:

294

European-Non Finnish (NFE)

AF:

0.974

AC:

66228

AN:

68026

Other (OTH)

AF:

0.966

AC:

2045

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

230

460

689

919

1149

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

912

1824

2736

3648

4560

<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:

0.974

Hom.:

8966

Bravo

AF:

0.976

Asia WGS

AF:

0.900

AC:

3130

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.5

(source)

DANN

Benign

0.53

PhyloP100

0.28

Mutation Taster

=100/0

polymorphism (auto)

(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

Computational scores

Splicing

Publications

Other links and lift over