rs34160967

Variant names:

• chr1-6575246-G-A
• rs34160967
• NM_138697.4:c.1114G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-6575246-G-A
• chr1-6575246-G-C

Variant summary

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

The NM_138697.4(TAS1R1):​c.1114G>A​(p.Ala372Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,613,466 control chromosomes in the GnomAD database, including 16,835 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1389 hom., cov: 33)
  • Exomes 𝑓: 0.14 (15446 hom.)
• Consequence: TAS1R1 NM_138697.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 33 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 (MetaRNN=0.002396077).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R1	NM_138697.4	c.1114G>A	p.Ala372Thr	missense_variant	Exon 3 of 6	ENST00000333172.11	NP_619642.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R1	ENST00000333172.11	c.1114G>A	p.Ala372Thr	missense_variant	Exon 3 of 6	1	NM_138697.4	ENSP00000331867.6
TAS1R1	ENST00000415267.1	c.274-1169G>A		intron_variant	Intron 1 of 3	1		ENSP00000408448.1
TAS1R1	ENST00000411823.5	c.889G>A	p.Ala297Thr	missense_variant	Exon 2 of 3	2		ENSP00000414166.1
TAS1R1	ENST00000351136.7	c.499-1169G>A		intron_variant	Intron 2 of 4	2		ENSP00000312558.5

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18302 AN: 152184 Hom.: 1390 Cov.: 33

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.0835

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.0970

GnomAD2 exomes AF: 0.131 AC: 32862 AN: 250040 AF XY: 0.131

Gnomad AFR exome AF: 0.0698

Gnomad AMR exome AF: 0.0502

Gnomad ASJ exome AF: 0.0805

Gnomad EAS exome AF: 0.313

Gnomad FIN exome AF: 0.218

Gnomad NFE exome AF: 0.133

Gnomad OTH exome AF: 0.111

GnomAD4 exome AF: 0.136 AC: 198466 AN: 1461164 Hom.: 15446 Cov.: 36 AF XY: 0.135 AC XY: 97998 AN XY: 726886

African (AFR) AF: 0.0697 AC: 2334 AN: 33474

American (AMR) AF: 0.0516 AC: 2308 AN: 44712

Ashkenazi Jewish (ASJ) AF: 0.0839 AC: 2193 AN: 26134

East Asian (EAS) AF: 0.346 AC: 13753 AN: 39700

South Asian (SAS) AF: 0.0983 AC: 8482 AN: 86254

European-Finnish (FIN) AF: 0.215 AC: 11350 AN: 52752

Middle Eastern (MID) AF: 0.0411 AC: 237 AN: 5768

European-Non Finnish (NFE) AF: 0.135 AC: 150029 AN: 1111980

Other (OTH) AF: 0.129 AC: 7780 AN: 60390

GnomAD4 genome AF: 0.120 AC: 18301 AN: 152302 Hom.: 1389 Cov.: 33 AF XY: 0.122 AC XY: 9093 AN XY: 74472

African (AFR) AF: 0.0703 AC: 2921 AN: 41580

American (AMR) AF: 0.0741 AC: 1135 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0835 AC: 290 AN: 3472

East Asian (EAS) AF: 0.312 AC: 1612 AN: 5168

South Asian (SAS) AF: 0.0989 AC: 478 AN: 4832

European-Finnish (FIN) AF: 0.216 AC: 2294 AN: 10618

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9255 AN: 68004

Other (OTH) AF: 0.0979 AC: 207 AN: 2114

Alfa AF: 0.129 Hom.: 2972

Bravo AF: 0.109

TwinsUK AF: 0.122 AC: 453

ALSPAC AF: 0.141 AC: 543

ESP6500AA AF: 0.0690 AC: 304

ESP6500EA AF: 0.126 AC: 1080

ExAC AF: 0.133 AC: 16172

Asia WGS AF: 0.182 AC: 634 AN: 3478

EpiCase AF: 0.122

EpiControl AF: 0.111

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.083
BayesDel_addAF	Benign	-0.50	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	0.54
DANN	Benign	0.76
DEOGEN2	Benign	0.054	T
Eigen	Benign	-0.81
Eigen_PC	Benign	-0.93
FATHMM_MKL	Benign	0.0069	N
LIST_S2	Benign	0.54	T
MetaRNN	Benign	0.0024	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	0.40	N
PhyloP100		0.22
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-0.65	N
REVEL	Benign	0.26
Sift	Benign	0.43	T
Sift4G	Benign	0.67	T
Polyphen		0.16	B
Vest4		0.073
MPC		0.17
ClinPred		0.0020	T
GERP RS		-0.64
Varity_R		0.050
gMVP		0.11
Mutation Taster		=99/1	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: rs34160967; hg19: chr1-6635306; COSMIC: COSV59839307; COSMIC: COSV59839307;