1-6571371-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138697.4(TAS1R1):c.498+156C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,174 control chromosomes in the GnomAD database, including 47,202 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 0.78 (47202 hom., cov: 32)
• Consequence: TAS1R1 NM_138697.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57

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]

LOC107984912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS1R1	NM_138697.4	c.498+156C>T		intron_variant		ENST00000333172.11
LOC107984912	XR_002958250.1	n.88-1388G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS1R1	ENST00000333172.11	c.498+156C>T		intron_variant		1	NM_138697.4	P1
TAS1R1	ENST00000415267.1	c.275+156C>T		intron_variant		1
TAS1R1	ENST00000351136.7	c.498+156C>T		intron_variant		2
TAS1R1	ENST00000411823.5	c.275+156C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.776 AC: 117959 AN: 152056 Hom.: 47193 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.832

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.794

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.775 AC: 117999 AN: 152174 Hom.: 47202 Cov.: 32 AF XY: 0.777 AC XY: 57779 AN XY: 74394

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.832

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.792

Alfa AF: 0.847 Hom.: 97832

Bravo AF: 0.764

Asia WGS AF: 0.762 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.13
Dann	Benign	0.61

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

Other links and lift over

dbSNP: rs11587438; hg19: chr1-6631431;