NM_138697.4:c.498+156C>T

Variant names:

• chr1-6571371-C-T
• rs11587438
• NM_138697.4:c.498+156C>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.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
• Publications: 17 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]

LOC107984912 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TAS1R1	NM_138697.4	c.498+156C>T		intron_variant	Intron 2 of 5	ENST00000333172.11	NP_619642.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R1	ENST00000333172.11	c.498+156C>T		intron_variant	Intron 2 of 5	1	NM_138697.4	ENSP00000331867.6
TAS1R1	ENST00000415267.1	c.273+156C>T		intron_variant	Intron 1 of 3	1		ENSP00000408448.1
TAS1R1	ENST00000351136.7	c.498+156C>T		intron_variant	Intron 2 of 4	2		ENSP00000312558.5
TAS1R1	ENST00000411823.5	c.273+156C>T		intron_variant	Intron 1 of 2	2		ENSP00000414166.1

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

African (AFR) AF: 0.562 AC: 23325 AN: 41500

American (AMR) AF: 0.839 AC: 12835 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.832 AC: 2889 AN: 3472

East Asian (EAS) AF: 0.804 AC: 4156 AN: 5168

South Asian (SAS) AF: 0.790 AC: 3813 AN: 4826

European-Finnish (FIN) AF: 0.874 AC: 9267 AN: 10602

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.869 AC: 59107 AN: 67988

Other (OTH) AF: 0.792 AC: 1673 AN: 2112

Alfa AF: 0.836 Hom.: 209358

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
PhyloP100		-2.6
PromoterAI		0.00010	Neutral
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: rs11587438; hg19: chr1-6631431;