rs11134371

Variant names:

• chr5-9792046-G-A
• rs11134371
• ENST00000511616.5:n.522-26353C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-9792046-G-A
• chr5-9792046-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001386348.1(TAS2R1):​c.-841-77807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,026 control chromosomes in the GnomAD database, including 16,212 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 0.44 (16212 hom., cov: 32)
• Consequence: TAS2R1 NM_001386348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

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]

ENSG00000286556 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R1	NM_001386348.1	c.-841-77807C>T		intron_variant	Intron 4 of 9		NP_001373277.1
LINC02112	NR_027112.2	n.520-26353C>T		intron_variant	Intron 4 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02112	ENST00000511616.5	n.522-26353C>T		intron_variant	Intron 4 of 12	1
ENSG00000286556	ENST00000669717.1	n.55-1930C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66525 AN: 151906 Hom.: 16182 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.438 AC: 66603 AN: 152026 Hom.: 16212 Cov.: 32 AF XY: 0.436 AC XY: 32379 AN XY: 74310

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.461

Alfa AF: 0.372 Hom.: 9157

Bravo AF: 0.452

Asia WGS AF: 0.465 AC: 1615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11134371; hg19: chr5-9792158;