NM_138697.4:c.192-7470C>T

Variant names:

• chr1-6563439-C-T
• rs4908563
• NM_138697.4:c.192-7470C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138697.4(TAS1R1):​c.192-7470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 152,092 control chromosomes in the GnomAD database, including 18,574 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 0.46 (18574 hom., cov: 33)
• Consequence: TAS1R1 NM_138697.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 9 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138697.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R1	NM_138697.4	MANE Select	c.192-7470C>T		intron	N/A	NP_619642.2
	TAS1R1	NM_177540.3		c.192-7470C>T		intron	N/A	NP_803884.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R1	ENST00000333172.11	TSL:1 MANE Select	c.192-7470C>T		intron	N/A	ENSP00000331867.6
	TAS1R1	ENST00000351136.7	TSL:2	c.192-7470C>T		intron	N/A	ENSP00000312558.5

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69691 AN: 151974 Hom.: 18568 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.458 AC: 69704 AN: 152092 Hom.: 18574 Cov.: 33 AF XY: 0.461 AC XY: 34298 AN XY: 74332

African (AFR) AF: 0.171 AC: 7114 AN: 41510

American (AMR) AF: 0.611 AC: 9334 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1902 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2257 AN: 5156

South Asian (SAS) AF: 0.564 AC: 2721 AN: 4822

European-Finnish (FIN) AF: 0.543 AC: 5724 AN: 10550

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38961 AN: 67976

Other (OTH) AF: 0.497 AC: 1051 AN: 2114

Alfa AF: 0.536 Hom.: 42503

Bravo AF: 0.451

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.9
DANN	Benign	0.48
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4908563; hg19: chr1-6623499;