rs16883317

chr5-9648480-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_027112.2(LINC02112):n.1585-6539G>A variant causes a intron, non coding transcript 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: LINC02112 NR_027112.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.187

Genes affected

(HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 69 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02112	NR_027112.2	n.1585-6539G>A		intron_variant, non_coding_transcript_variant
TAS2R1	NM_001386348.1	c.-81+10941G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000504182.2	n.35+9944G>A		intron_variant, non_coding_transcript_variant		5
LINC02112	ENST00000511616.5	n.1587-6539G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.0203

Gnomad4 AMR AF: 0.0229

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.000582

Gnomad4 SAS AF: 0.0366

Gnomad4 FIN AF: 0.0261

Gnomad4 NFE AF: 0.0326

Gnomad4 OTH AF: 0.0303

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16883317; hg19: chr5-9648592;