7-141764965-C-T

Variant names:

• chr7-141764965-C-T
• rs2270009
• NM_016943.2:c.807C>T

Variant summary

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

The NM_016943.2(TAS2R3):​c.807C>T​(p.Gly269Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 1,613,878 control chromosomes in the GnomAD database, including 185,168 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 0.42 (14387 hom., cov: 33)
  • Exomes 𝑓: 0.48 (170781 hom.)
• Consequence: TAS2R3 NM_016943.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.306
• Publications: 33 publications found

Genes affected

TAS2R3 (HGNC:14910): (taste 2 receptor member 3) This gene encodes a member of a family of candidate taste receptors that are members of the G protein-coupled receptor superfamily and that are specifically expressed by taste receptor cells of the tongue and palate epithelia. These apparently intronless taste receptor genes encode a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered with another 3 candidate taste receptor genes in chromosome 7 and is genetically linked to loci that influence bitter perception. [provided by RefSeq, Jul 2008]

SSBP1 (HGNC:11317): (single stranded DNA binding protein 1) SSBP1 is a housekeeping gene involved in mitochondrial biogenesis (Tiranti et al., 1995 [PubMed 7789991]). It is also a subunit of a single-stranded DNA (ssDNA)-binding complex involved in the maintenance of genome stability (Huang et al., 2009) [PubMed 19683501].[supplied by OMIM, Feb 2010]

SSBP1 Gene-Disease associations (from GenCC):

• optic atrophy 13 with retinal and foveal abnormalities

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: ClinGen, Ambry Genetics
• Leigh syndrome

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

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=-0.306 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R3	NM_016943.2	c.807C>T	p.Gly269Gly	synonymous_variant	Exon 1 of 1	ENST00000247879.2	NP_058639.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R3	ENST00000247879.2	c.807C>T	p.Gly269Gly	synonymous_variant	Exon 1 of 1	6	NM_016943.2	ENSP00000247879.2
SSBP1	ENST00000465582.5	c.*30+14581C>T		intron_variant	Intron 7 of 7	5		ENSP00000420485.1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63736 AN: 151914 Hom.: 14380 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.449

GnomAD2 exomes AF: 0.476 AC: 119743 AN: 251406 AF XY: 0.480

Gnomad AFR exome AF: 0.221

Gnomad AMR exome AF: 0.489

Gnomad ASJ exome AF: 0.456

Gnomad EAS exome AF: 0.691

Gnomad FIN exome AF: 0.460

Gnomad NFE exome AF: 0.485

Gnomad OTH exome AF: 0.491

GnomAD4 exome AF: 0.481 AC: 702447 AN: 1461844 Hom.: 170781 Cov.: 71 AF XY: 0.482 AC XY: 350249 AN XY: 727218

African (AFR) AF: 0.219 AC: 7339 AN: 33480

American (AMR) AF: 0.494 AC: 22075 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 11828 AN: 26136

East Asian (EAS) AF: 0.674 AC: 26773 AN: 39700

South Asian (SAS) AF: 0.453 AC: 39074 AN: 86254

European-Finnish (FIN) AF: 0.462 AC: 24658 AN: 53420

Middle Eastern (MID) AF: 0.474 AC: 2736 AN: 5768

European-Non Finnish (NFE) AF: 0.485 AC: 538801 AN: 1111972

Other (OTH) AF: 0.483 AC: 29163 AN: 60394

GnomAD4 genome AF: 0.419 AC: 63772 AN: 152034 Hom.: 14387 Cov.: 33 AF XY: 0.422 AC XY: 31377 AN XY: 74308

African (AFR) AF: 0.233 AC: 9640 AN: 41452

American (AMR) AF: 0.488 AC: 7467 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1614 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3539 AN: 5158

South Asian (SAS) AF: 0.441 AC: 2127 AN: 4818

European-Finnish (FIN) AF: 0.461 AC: 4873 AN: 10560

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.488 AC: 33185 AN: 67972

Other (OTH) AF: 0.455 AC: 961 AN: 2114

Alfa AF: 0.470 Hom.: 32552

Bravo AF: 0.416

Asia WGS AF: 0.552 AC: 1917 AN: 3478

EpiCase AF: 0.495

EpiControl AF: 0.495

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.9
DANN	Benign	0.59
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs2270009; hg19: chr7-141464765; COSMIC: COSV56092845;