1-1334979-T-C

Variant names:

• chr1-1334979-T-C
• rs307374
• NM_152228.3:c.*515T>C

Variant summary

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

The NM_152228.3(TAS1R3):​c.*515T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.97 in 155,226 control chromosomes in the GnomAD database, including 73,124 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 0.97 (71773 hom., cov: 36)
  • Exomes 𝑓: 0.97 (1351 hom.)
• Consequence: TAS1R3 NM_152228.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919
• Publications: 2 publications found

Genes affected

TAS1R3 (HGNC:15661): (taste 1 receptor member 3) The protein encoded by this gene is a G-protein coupled receptor involved in taste responses. The encoded protein can form a heterodimeric receptor with TAS1R1 to elicit the umami taste response, or it can bind with TAS1R2 to form a receptor for the sweet taste response. [provided by RefSeq, Nov 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152228.3. 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
	TAS1R3	NM_152228.3	MANE Select	c.*515T>C		3_prime_UTR	Exon 6 of 6	NP_689414.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R3	ENST00000339381.6	TSL:2 MANE Select	c.*515T>C		3_prime_UTR	Exon 6 of 6	ENSP00000344411.5

Frequencies

GnomAD3 genomes AF: 0.970 AC: 147716 AN: 152222 Hom.: 71717 Cov.: 36

Gnomad AFR AF: 0.988

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.977

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.967

GnomAD4 exome AF: 0.966 AC: 2789 AN: 2886 Hom.: 1351 Cov.: 0 AF XY: 0.965 AC XY: 1413 AN XY: 1464

African (AFR) AF: 1.00 AC: 34 AN: 34

American (AMR) AF: 0.965 AC: 440 AN: 456

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 25 AN: 26

East Asian (EAS) AF: 0.923 AC: 24 AN: 26

South Asian (SAS) AF: 0.884 AC: 152 AN: 172

European-Finnish (FIN) AF: 0.900 AC: 36 AN: 40

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.975 AC: 1973 AN: 2024

Other (OTH) AF: 0.972 AC: 105 AN: 108

GnomAD4 genome AF: 0.970 AC: 147832 AN: 152340 Hom.: 71773 Cov.: 36 AF XY: 0.967 AC XY: 72041 AN XY: 74476

African (AFR) AF: 0.988 AC: 41093 AN: 41586

American (AMR) AF: 0.980 AC: 15003 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.977 AC: 3392 AN: 3472

East Asian (EAS) AF: 0.908 AC: 4693 AN: 5168

South Asian (SAS) AF: 0.915 AC: 4418 AN: 4830

European-Finnish (FIN) AF: 0.923 AC: 9804 AN: 10620

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66231 AN: 68030

Other (OTH) AF: 0.966 AC: 2045 AN: 2116

Alfa AF: 0.974 Hom.: 8966

Bravo AF: 0.976

Asia WGS AF: 0.900 AC: 3132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.10
DANN	Benign	0.49
PhyloP100		-0.92
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: rs307374; hg19: chr1-1270359;