Genetic Variant TAS1R1:c.1261-14C>T (chr1-6576401-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_138697.4(TAS1R1):c.1261-14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 1,613,302 control chromosomes in the GnomAD database, including 200,386 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 0.44 ( 15837 hom., cov: 32)

Exomes 𝑓: 0.50 ( 184549 hom. )

Consequence

TAS1R1
NM_138697.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

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 (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R1	NM_138697.4 link	c.1261-14C>T		intron_variant	Intron 3 of 5	ENST00000333172.11	NP_619642.2	Q7RTX1-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TAS1R1	ENST00000333172.11 link	c.1261-14C>T	intron_variant	Intron 3 of 5	1	NM_138697.4	ENSP00000331867.6	Q7RTX1-1
TAS1R1	ENST00000415267.1 link	c.274-14C>T	intron_variant	Intron 1 of 3	1		ENSP00000408448.1	H0Y6X0
TAS1R1	ENST00000351136.7 link	c.499-14C>T	intron_variant	Intron 2 of 4	2		ENSP00000312558.5	Q7RTX1-2
TAS1R1	ENST00000411823.5 link	c.1035+1009C>T	intron_variant	Intron 2 of 2	2		ENSP00000414166.1	H7C3W7

Frequencies

GnomAD3 genomes

AF:

0.442

AC:

67161

AN:

151902

Hom.:

15831

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.512

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.483

Gnomad EAS

AF:

0.338

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.600

Gnomad MID

AF:

0.350

Gnomad NFE

AF:

0.518

Gnomad OTH

AF:

0.427

GnomAD3 exomes

AF:

0.482

AC:

121163

AN:

251356

Hom.:

30367

AF XY:

0.478

AC XY:

64932

AN XY:

135854

show subpopulations

Gnomad AFR exome

AF:

0.277

Gnomad AMR exome

AF:

0.566

Gnomad ASJ exome

AF:

0.471

Gnomad EAS exome

AF:

0.335

Gnomad SAS exome

AF:

0.400

Gnomad FIN exome

AF:

0.597

Gnomad NFE exome

AF:

0.512

Gnomad OTH exome

AF:

0.466

GnomAD4 exome

AF:

0.498

AC:

728383

AN:

1461282

Hom.:

184549

Cov.:

AF XY:

0.496

AC XY:

360582

AN XY:

726946

show subpopulations

Gnomad4 AFR exome

AF:

0.269

Gnomad4 AMR exome

AF:

0.551

Gnomad4 ASJ exome

AF:

0.467

Gnomad4 EAS exome

AF:

0.362

Gnomad4 SAS exome

AF:

0.400

Gnomad4 FIN exome

AF:

0.587

Gnomad4 NFE exome

AF:

0.514

Gnomad4 OTH exome

AF:

0.470

GnomAD4 genome

AF:

0.442

AC:

67186

AN:

152020

Hom.:

15837

Cov.:

AF XY:

0.443

AC XY:

32944

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.278

Gnomad4 AMR

AF:

0.485

Gnomad4 ASJ

AF:

0.483

Gnomad4 EAS

AF:

0.338

Gnomad4 SAS

AF:

0.382

Gnomad4 FIN

AF:

0.600

Gnomad4 NFE

AF:

0.518

Gnomad4 OTH

AF:

0.425

Alfa

AF:

0.396

Hom.:

1936

Bravo

AF:

0.430

Asia WGS

AF:

0.351

AC:

1223

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.18

DANN

Benign

0.69

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