5-9629417-G-C

Variant names:

• chr5-9629417-G-C
• rs2234233
• NM_019599.3:c.616C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_019599.3(TAS2R1):​c.616C>G​(p.Arg206Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R206Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TAS2R1 NM_019599.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132
• Publications: 0 publications found

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]

ENSG00000248525 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17148617).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R1	NM_019599.3	c.616C>G	p.Arg206Gly	missense_variant	Exon 1 of 1	ENST00000382492.4	NP_062545.1
TAS2R1	NM_001386348.1	c.496C>G	p.Arg166Gly	missense_variant	Exon 10 of 10		NP_001373277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R1	ENST00000382492.4	c.616C>G	p.Arg206Gly	missense_variant	Exon 1 of 1	6	NM_019599.3	ENSP00000371932.2
ENSG00000248525	ENST00000504182.2	n.36-5815C>G		intron_variant	Intron 1 of 2	5
TAS2R1	ENST00000514078.1	c.*29C>G		downstream_gene_variant		3		ENSP00000476190.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	0.39
DANN	Benign	0.75
DEOGEN2	Benign	0.028	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.041	N
LIST_S2	Benign	0.59	T
M_CAP	Benign	0.0069	T
MetaRNN	Benign	0.17	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.6	L
PhyloP100		-0.13
PrimateAI	Benign	0.16	T
PROVEAN	Uncertain	-3.3	D
REVEL	Benign	0.057
Sift	Benign	0.11	T
Sift4G	Benign	0.12	T
Polyphen		0.35	B
Vest4		0.25
MutPred		0.61		Loss of MoRF binding (P = 0.0176);
MVP		0.17
MPC		0.045
ClinPred		0.23	T
GERP RS		-11
Varity_R		0.10
gMVP		0.10
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2234233; hg19: chr5-9629529;