12-11186144-C-T

Position:

• chr12-11186144-C-T

Variant summary

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

The NM_181429.2(TAS2R42):​c.794G>A​(p.Cys265Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 1,613,684 control chromosomes in the GnomAD database, including 461,752 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.76 (44199 hom., cov: 32)
  • Exomes 𝑓: 0.76 (417553 hom.)
• Consequence: TAS2R42 NM_181429.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

TAS2R42 (HGNC:18888): (taste 2 receptor member 42) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway and sensory perception of taste. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0069088936).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R42	NM_181429.2	c.794G>A	p.Cys265Tyr	missense_variant	1/1	ENST00000334266.1	NP_852094.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS2R42	ENST00000334266.1	c.794G>A	p.Cys265Tyr	missense_variant	1/1	6	NM_181429.2	ENSP00000334050.1

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115825 AN: 152008 Hom.: 44153 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.773

GnomAD4 exome AF: 0.755 AC: 1104134 AN: 1461558 Hom.: 417553 Cov.: 58 AF XY: 0.756 AC XY: 550009 AN XY: 727084

Gnomad4 AFR exome AF: 0.759

Gnomad4 AMR exome AF: 0.753

Gnomad4 ASJ exome AF: 0.808

Gnomad4 EAS exome AF: 0.777

Gnomad4 SAS exome AF: 0.787

Gnomad4 FIN exome AF: 0.745

Gnomad4 NFE exome AF: 0.751

Gnomad4 OTH exome AF: 0.761

GnomAD4 genome AF: 0.762 AC: 115924 AN: 152126 Hom.: 44199 Cov.: 32 AF XY: 0.760 AC XY: 56558 AN XY: 74384

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.771

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.775

Alfa AF: 0.763 Hom.: 91464

Bravo AF: 0.765

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.0030
MetaRNN	Benign	0.0069	T
Sift4G	Benign	1.0	T
Vest4		0.037
gMVP		0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1451772; hg19: -;