rs3813210

Variant names:

• chr1-1332779-C-T
• rs3813210
• NM_152228.3:c.1248C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_152228.3(TAS1R3):​c.1248C>T​(p.Pro416Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0643 in 1,605,362 control chromosomes in the GnomAD database, including 5,835 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 0.12 (1824 hom., cov: 34)
  • Exomes 𝑓: 0.059 (4011 hom.)
• Consequence: TAS1R3 NM_152228.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 10 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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP7: Synonymous conserved (PhyloP=-1.93 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R3	NM_152228.3	c.1248C>T	p.Pro416Pro	synonymous_variant	Exon 3 of 6	ENST00000339381.6	NP_689414.2
TAS1R3	XM_017002435.2	c.1248C>T	p.Pro416Pro	synonymous_variant	Exon 3 of 5		XP_016857924.1
TAS1R3	XM_017002436.2	c.1248C>T	p.Pro416Pro	synonymous_variant	Exon 3 of 5		XP_016857925.1
TAS1R3	XM_047431571.1	c.1248C>T	p.Pro416Pro	synonymous_variant	Exon 3 of 6		XP_047287527.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R3	ENST00000339381.6	c.1248C>T	p.Pro416Pro	synonymous_variant	Exon 3 of 6	2	NM_152228.3	ENSP00000344411.5

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17981 AN: 152180 Hom.: 1818 Cov.: 34

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.0744

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.110

GnomAD2 exomes AF: 0.0884 AC: 21322 AN: 241272 AF XY: 0.0801

Gnomad AFR exome AF: 0.282

Gnomad AMR exome AF: 0.176

Gnomad ASJ exome AF: 0.0621

Gnomad EAS exome AF: 0.0908

Gnomad FIN exome AF: 0.0547

Gnomad NFE exome AF: 0.0456

Gnomad OTH exome AF: 0.0732

GnomAD4 exome AF: 0.0587 AC: 85230 AN: 1453064 Hom.: 4011 Cov.: 81 AF XY: 0.0579 AC XY: 41848 AN XY: 722824

African (AFR) AF: 0.287 AC: 9589 AN: 33450

American (AMR) AF: 0.165 AC: 7367 AN: 44602

Ashkenazi Jewish (ASJ) AF: 0.0635 AC: 1656 AN: 26082

East Asian (EAS) AF: 0.0729 AC: 2891 AN: 39634

South Asian (SAS) AF: 0.0748 AC: 6447 AN: 86184

European-Finnish (FIN) AF: 0.0597 AC: 2791 AN: 46726

Middle Eastern (MID) AF: 0.0589 AC: 339 AN: 5758

European-Non Finnish (NFE) AF: 0.0447 AC: 49581 AN: 1110390

Other (OTH) AF: 0.0758 AC: 4569 AN: 60238

GnomAD4 genome AF: 0.118 AC: 18022 AN: 152298 Hom.: 1824 Cov.: 34 AF XY: 0.116 AC XY: 8618 AN XY: 74484

African (AFR) AF: 0.276 AC: 11481 AN: 41534

American (AMR) AF: 0.110 AC: 1677 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0689 AC: 239 AN: 3470

East Asian (EAS) AF: 0.0947 AC: 491 AN: 5184

South Asian (SAS) AF: 0.0745 AC: 360 AN: 4832

European-Finnish (FIN) AF: 0.0506 AC: 538 AN: 10624

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0436 AC: 2966 AN: 68026

Other (OTH) AF: 0.110 AC: 233 AN: 2114

Alfa AF: 0.0736 Hom.: 416

Bravo AF: 0.132

Asia WGS AF: 0.0990 AC: 344 AN: 3478

EpiCase AF: 0.0417

EpiControl AF: 0.0427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.1
DANN	Benign	0.75
PhyloP100		-1.9
Mutation Taster		=29/71	disease causing

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: rs3813210; hg19: chr1-1268159; COSMIC: COSV59563545; COSMIC: COSV59563545;