NM_152228.3:c.*485A>G

Variant names:

• chr1-1334949-A-G
• rs188647
• NM_152228.3:c.*485A>G

Variant summary

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

The NM_152228.3(TAS1R3):​c.*485A>G 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 156,970 control chromosomes in the GnomAD database, including 73,948 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 (71763 hom., cov: 36)
  • Exomes 𝑓: 0.97 (2185 hom.)
• Consequence: TAS1R3 NM_152228.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 1 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=-0.84).
• 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R3	NM_152228.3	MANE Select	c.*485A>G		3_prime_UTR	Exon 6 of 6	NP_689414.2	Q7RTX0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS1R3	ENST00000339381.6	TSL:2 MANE Select	c.*485A>G		3_prime_UTR	Exon 6 of 6	ENSP00000344411.5	Q7RTX0

Frequencies

GnomAD3 genomes AF: 0.970 AC: 147699 AN: 152208 Hom.: 71707 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: 0.907

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: 0.970 AC: 4503 AN: 4644 Hom.: 2185 Cov.: 0 AF XY: 0.967 AC XY: 2283 AN XY: 2360

African (AFR) AF: 1.00 AC: 70 AN: 70

American (AMR) AF: 0.977 AC: 719 AN: 736

Ashkenazi Jewish (ASJ) AF: 0.987 AC: 75 AN: 76

East Asian (EAS) AF: 0.971 AC: 66 AN: 68

South Asian (SAS) AF: 0.888 AC: 229 AN: 258

European-Finnish (FIN) AF: 0.907 AC: 78 AN: 86

Middle Eastern (MID) AF: 1.00 AC: 6 AN: 6

European-Non Finnish (NFE) AF: 0.975 AC: 3047 AN: 3126

Other (OTH) AF: 0.977 AC: 213 AN: 218

GnomAD4 genome AF: 0.970 AC: 147815 AN: 152326 Hom.: 71763 Cov.: 36 AF XY: 0.967 AC XY: 72042 AN XY: 74478

African (AFR) AF: 0.988 AC: 41083 AN: 41578

American (AMR) AF: 0.980 AC: 14999 AN: 15306

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

East Asian (EAS) AF: 0.907 AC: 4690 AN: 5170

South Asian (SAS) AF: 0.914 AC: 4417 AN: 4830

European-Finnish (FIN) AF: 0.923 AC: 9808 AN: 10622

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

European-Non Finnish (NFE) AF: 0.974 AC: 66228 AN: 68026

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: 3130 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.53
PhyloP100		0.28
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: rs188647; hg19: chr1-1270329;