rs35969491

Variant names:

• chr12-11186414-T-A
• rs35969491
• NM_181429.2:c.524A>T

Your query was ambiguous. Multiple possible variants found:

• chr12-11186414-T-A
• chr12-11186414-T-C
• chr12-11186414-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181429.2(TAS2R42):​c.524A>T​(p.Tyr175Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 1,600,074 control chromosomes in the GnomAD database, including 281,843 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.51 (22034 hom., cov: 32)
  • Exomes 𝑓: 0.59 (259809 hom.)
• Consequence: TAS2R42 NM_181429.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 36 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=2.9399787E-6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181429.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R42	NM_181429.2	MANE Select	c.524A>T	p.Tyr175Phe	missense	Exon 1 of 1	NP_852094.2	Q7RTR8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R42	ENST00000334266.1	TSL:6 MANE Select	c.524A>T	p.Tyr175Phe	missense	Exon 1 of 1	ENSP00000334050.1	Q7RTR8

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77067 AN: 151924 Hom.: 22030 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.543

GnomAD2 exomes AF: 0.610 AC: 150197 AN: 246358 AF XY: 0.616

Gnomad AFR exome AF: 0.215

Gnomad AMR exome AF: 0.634

Gnomad ASJ exome AF: 0.649

Gnomad EAS exome AF: 0.753

Gnomad FIN exome AF: 0.671

Gnomad NFE exome AF: 0.604

Gnomad OTH exome AF: 0.614

GnomAD4 exome AF: 0.594 AC: 860515 AN: 1448030 Hom.: 259809 Cov.: 39 AF XY: 0.597 AC XY: 430703 AN XY: 721112

African (AFR) AF: 0.206 AC: 6796 AN: 32912

American (AMR) AF: 0.634 AC: 27661 AN: 43624

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 16885 AN: 25832

East Asian (EAS) AF: 0.752 AC: 29776 AN: 39596

South Asian (SAS) AF: 0.653 AC: 55866 AN: 85592

European-Finnish (FIN) AF: 0.665 AC: 35451 AN: 53308

Middle Eastern (MID) AF: 0.645 AC: 3672 AN: 5690

European-Non Finnish (NFE) AF: 0.589 AC: 649086 AN: 1101648

Other (OTH) AF: 0.590 AC: 35322 AN: 59828

GnomAD4 genome AF: 0.507 AC: 77078 AN: 152044 Hom.: 22034 Cov.: 32 AF XY: 0.515 AC XY: 38259 AN XY: 74338

African (AFR) AF: 0.222 AC: 9216 AN: 41508

American (AMR) AF: 0.596 AC: 9109 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2259 AN: 3468

East Asian (EAS) AF: 0.743 AC: 3825 AN: 5146

South Asian (SAS) AF: 0.648 AC: 3118 AN: 4810

European-Finnish (FIN) AF: 0.666 AC: 7037 AN: 10562

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40536 AN: 67950

Other (OTH) AF: 0.546 AC: 1156 AN: 2116

Alfa AF: 0.583 Hom.: 18668

Bravo AF: 0.491

TwinsUK AF: 0.590 AC: 2189

ALSPAC AF: 0.582 AC: 2243

ESP6500AA AF: 0.214 AC: 926

ESP6500EA AF: 0.595 AC: 5079

ExAC AF: 0.600 AC: 72657

Asia WGS AF: 0.651 AC: 2260 AN: 3478

EpiCase AF: 0.608

EpiControl AF: 0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.72	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	11
DANN	Benign	0.93
Eigen	Benign	-0.50
Eigen_PC	Benign	-0.71
FATHMM_MKL	Benign	0.078	N
MetaRNN	Benign	0.0000029	T
MetaSVM	Benign	-0.98	T
PhyloP100		0.083
PrimateAI	Benign	0.31	T
PROVEAN	Uncertain	-2.5	D
REVEL	Benign	0.063
Sift	Benign	0.099	T
Sift4G	Benign	0.074	T
Vest4		0.081
MPC		0.047
ClinPred		0.025	T
GERP RS		1.5
gMVP		0.078
Mutation Taster		=97/3	polymorphism (auto)

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: rs35969491; hg19: chr12-11339020; COSMIC: COSV62084971;