chr7-122995846-T-C

Variant names:

• chr7-122995846-T-C
• rs978739
• NM_016945.3:c.-212A>G

Variant summary

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

The NM_016945.3(TAS2R16):​c.-212A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 489,260 control chromosomes in the GnomAD database, including 32,486 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 0.37 (10387 hom., cov: 32)
  • Exomes 𝑓: 0.36 (22099 hom.)
• Consequence: TAS2R16 NM_016945.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 20 publications found

Genes affected

TAS2R16 (HGNC:14921): (taste 2 receptor member 16) This gene encodes a member of a family of candidate taste receptors that are members of the G protein-coupled receptor superfamily. These family members are specifically expressed by taste receptor cells of the tongue and palate epithelia. Each of these apparently intronless genes encodes 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R16	NM_016945.3	c.-212A>G		upstream_gene_variant		ENST00000249284.3	NP_058641.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R16	ENST00000249284.3	c.-212A>G		upstream_gene_variant		6	NM_016945.3	ENSP00000249284.2

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55431 AN: 151806 Hom.: 10376 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.350

GnomAD4 exome AF: 0.356 AC: 120240 AN: 337336 Hom.: 22099 AF XY: 0.360 AC XY: 62135 AN XY: 172522

African (AFR) AF: 0.416 AC: 3550 AN: 8530

American (AMR) AF: 0.287 AC: 3088 AN: 10766

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 3503 AN: 10982

East Asian (EAS) AF: 0.342 AC: 8507 AN: 24894

South Asian (SAS) AF: 0.468 AC: 8546 AN: 18258

European-Finnish (FIN) AF: 0.380 AC: 8997 AN: 23680

Middle Eastern (MID) AF: 0.339 AC: 545 AN: 1606

European-Non Finnish (NFE) AF: 0.350 AC: 76200 AN: 217914

Other (OTH) AF: 0.353 AC: 7304 AN: 20706

GnomAD4 genome AF: 0.365 AC: 55474 AN: 151924 Hom.: 10387 Cov.: 32 AF XY: 0.366 AC XY: 27147 AN XY: 74248

African (AFR) AF: 0.400 AC: 16555 AN: 41434

American (AMR) AF: 0.292 AC: 4444 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1752 AN: 5154

South Asian (SAS) AF: 0.455 AC: 2195 AN: 4820

European-Finnish (FIN) AF: 0.404 AC: 4269 AN: 10568

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23996 AN: 67928

Other (OTH) AF: 0.355 AC: 750 AN: 2110

Alfa AF: 0.352 Hom.: 14263

Bravo AF: 0.356

Asia WGS AF: 0.417 AC: 1449 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.80
PhyloP100		-0.59
PromoterAI		0.018	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs978739; hg19: chr7-122635900;