rs16883317

Variant names:

• chr5-9648480-C-T
• rs16883317
• ENST00000511616.5:n.1587-6539G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001386348.1(TAS2R1):​c.-81+10941G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0273 in 152,050 control chromosomes in the GnomAD database, including 69 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 0.027 (69 hom., cov: 32)
• Consequence: TAS2R1 NM_001386348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187
• Publications: 4 publications found

Genes affected

LINC02112 (HGNC:27756): (long intergenic non-protein coding RNA 2112)

TAS2R1 (HGNC:14909): (taste 2 receptor member 1) 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. This intronless taste receptor gene encodes a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is mapped to chromosome 5p15, the location of a genetic locus (PROP) that controls the detection of the bitter compound 6-n-propyl-2-thiouracil. [provided by RefSeq, Jul 2008]

ENSG00000248525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0273 (4157/152050) while in subpopulation SAS AF = 0.0366 (176/4810). AF 95% confidence interval is 0.0322. There are 69 homozygotes in GnomAd4. There are 2049 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 69 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001386348.1. 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
	TAS2R1	NM_001386348.1		c.-81+10941G>A		intron	N/A	NP_001373277.1
	LINC02112	NR_027112.2		n.1585-6539G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02112	ENST00000511616.5	TSL:1	n.1587-6539G>A		intron	N/A
	LINC02112	ENST00000606744.1	TSL:1	n.66-6539G>A		intron	N/A
	TAS2R1	ENST00000514078.1	TSL:3	c.-80-18488G>A		intron	N/A	ENSP00000476190.1	U3KQT0

Frequencies

GnomAD3 genomes AF: 0.0273 AC: 4151 AN: 151932 Hom.: 69 Cov.: 32

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0229

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.000581

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0326

Gnomad OTH AF: 0.0301

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0273 AC: 4157 AN: 152050 Hom.: 69 Cov.: 32 AF XY: 0.0276 AC XY: 2049 AN XY: 74306

African (AFR) AF: 0.0203 AC: 841 AN: 41490

American (AMR) AF: 0.0229 AC: 350 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3472

East Asian (EAS) AF: 0.000582 AC: 3 AN: 5152

South Asian (SAS) AF: 0.0366 AC: 176 AN: 4810

European-Finnish (FIN) AF: 0.0261 AC: 276 AN: 10564

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0326 AC: 2215 AN: 67972

Other (OTH) AF: 0.0303 AC: 64 AN: 2114

Alfa AF: 0.0300 Hom.: 8

Bravo AF: 0.0268

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs16883317; hg19: chr5-9648592;