7-141764114-T-C

Variant names:

• chr7-141764114-T-C
• rs765007
• NM_016943.2:c.-45T>C

Variant summary

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

The NM_016943.2(TAS2R3):​c.-45T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 1,563,914 control chromosomes in the GnomAD database, including 202,803 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 0.52 (20437 hom., cov: 32)
  • Exomes 𝑓: 0.51 (182366 hom.)
• Consequence: TAS2R3 NM_016943.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 32 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, AR Classification: STRONG, MODERATE, LIMITED Submitted by: PanelApp Australia, ClinGen, Ambry Genetics
• Leigh syndrome

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016943.2. 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
	TAS2R3	NM_016943.2	MANE Select	c.-45T>C		5_prime_UTR	Exon 1 of 1	NP_058639.1	Q9NYW6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R3	ENST00000247879.2	TSL:6 MANE Select	c.-45T>C		5_prime_UTR	Exon 1 of 1	ENSP00000247879.2	Q9NYW6
	SSBP1	ENST00000465582.5	TSL:5	c.*30+13730T>C		intron	N/A	ENSP00000420485.1	Q04837

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78479 AN: 151914 Hom.: 20401 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.514

GnomAD2 exomes AF: 0.534 AC: 114273 AN: 214138 AF XY: 0.535

Gnomad AFR exome AF: 0.519

Gnomad AMR exome AF: 0.549

Gnomad ASJ exome AF: 0.466

Gnomad EAS exome AF: 0.754

Gnomad FIN exome AF: 0.481

Gnomad NFE exome AF: 0.491

Gnomad OTH exome AF: 0.528

GnomAD4 exome AF: 0.505 AC: 713574 AN: 1411882 Hom.: 182366 Cov.: 49 AF XY: 0.508 AC XY: 354494 AN XY: 697566

African (AFR) AF: 0.524 AC: 17056 AN: 32546

American (AMR) AF: 0.552 AC: 22619 AN: 40954

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 10639 AN: 23102

East Asian (EAS) AF: 0.770 AC: 30231 AN: 39282

South Asian (SAS) AF: 0.586 AC: 46212 AN: 78812

European-Finnish (FIN) AF: 0.481 AC: 20511 AN: 42618

Middle Eastern (MID) AF: 0.512 AC: 2829 AN: 5528

European-Non Finnish (NFE) AF: 0.489 AC: 532940 AN: 1090522

Other (OTH) AF: 0.522 AC: 30537 AN: 58518

GnomAD4 genome AF: 0.517 AC: 78573 AN: 152032 Hom.: 20437 Cov.: 32 AF XY: 0.520 AC XY: 38644 AN XY: 74298

African (AFR) AF: 0.525 AC: 21766 AN: 41462

American (AMR) AF: 0.546 AC: 8339 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3468

East Asian (EAS) AF: 0.751 AC: 3873 AN: 5156

South Asian (SAS) AF: 0.594 AC: 2863 AN: 4820

European-Finnish (FIN) AF: 0.482 AC: 5105 AN: 10582

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33496 AN: 67942

Other (OTH) AF: 0.518 AC: 1096 AN: 2114

Alfa AF: 0.503 Hom.: 50591

Bravo AF: 0.525

Asia WGS AF: 0.679 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.11
DANN	Benign	0.33
PhyloP100		-1.7
PromoterAI		0.038	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=300/0	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: rs765007; hg19: chr7-141463914; COSMIC: COSV107213637;