rs41467

chr5-9627977-A-Cchr5-9627977-A-T

Variant summary

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

The NM_019599.3(TAS2R1):c.*1156T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,630 control chromosomes in the GnomAD database, including 36,416 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 0.68 (36416 hom., cov: 32)
• Consequence: TAS2R1 NM_019599.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

Genes affected

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS2R1	NM_019599.3	c.*1156T>G		3_prime_UTR_variant	1/1	ENST00000382492.4
TAS2R1	NM_001386348.1	c.*1156T>G		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAS2R1	ENST00000382492.4	c.*1156T>G		3_prime_UTR_variant	1/1		NM_019599.3	P1
	ENST00000504182.2	n.36-4375T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102602 AN: 151512 Hom.: 36338 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.619

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.678 AC: 102742 AN: 151630 Hom.: 36416 Cov.: 32 AF XY: 0.680 AC XY: 50355 AN XY: 74084

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.672

Alfa AF: 0.622 Hom.: 5895

Bravo AF: 0.700

Asia WGS AF: 0.756 AC: 2626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.0
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41467; hg19: chr5-9628089;