1-1334979-T-C

Position:

• chr1-1334979-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS1R3	NM_152228.3	c.*515T>C		3_prime_UTR_variant	6/6	ENST00000339381.6
TAS1R3	XM_017002435.2	c.*515T>C		3_prime_UTR_variant	5/5
TAS1R3	XM_017002436.2	c.*515T>C		3_prime_UTR_variant	5/5
TAS1R3	XM_047431571.1	c.*515T>C		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS1R3	ENST00000339381.6	c.*515T>C		3_prime_UTR_variant	6/6	2	NM_152228.3	P1

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

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.965

Gnomad4 ASJ exome AF: 0.962

Gnomad4 EAS exome AF: 0.923

Gnomad4 SAS exome AF: 0.884

Gnomad4 FIN exome AF: 0.900

Gnomad4 NFE exome AF: 0.975

Gnomad4 OTH exome AF: 0.972

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

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.980

Gnomad4 ASJ AF: 0.977

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.966

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.10
DANN	Benign	0.49

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: rs307374; hg19: chr1-1270359;