Variant rs1404635 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_176883.2(TAS2R41):c.189G>A(p.Thr63Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,613,844 control chromosomes in the GnomAD database, including 60,774 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 0.22 ( 4429 hom., cov: 31)

Exomes 𝑓: 0.27 ( 56345 hom. )

Consequence

TAS2R41
NM_176883.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.143

Variant links:

Genes affected

TAS2R41 (HGNC:18883): (taste 2 receptor member 41) This gene encodes a member of the bitter taste receptor family which belong to the G protein-coupled receptor superfamily and are predominantly expressed in taste receptor cells of the tongue and palate epithelia. This intronless taste receptor gene encodes a seven-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered together with eight other taste receptor genes on chromosome 7. Chloramphenicol is an agonist for the encoded protein. [provided by RefSeq, Jul 2017]

TAS2R41 links:

EPHA1-AS1 (HGNC:):

EPHA1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP7

Synonymous conserved (PhyloP=0.143 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R41	NM_176883.2 linkuse as main transcript	c.189G>A	p.Thr63Thr	synonymous_variant	1/1	ENST00000408916.1	NP_795364.2	P59536
EPHA1-AS1	NR_033897.1 linkuse as main transcript	n.207-26713G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TAS2R41	ENST00000408916.1 linkuse as main transcript	c.189G>A	p.Thr63Thr	synonymous_variant	1/1	6	NM_176883.2	ENSP00000386201.1	P59536
EPHA1-AS1	ENST00000429289.5 linkuse as main transcript	n.207-26713G>A		intron_variant		1
EPHA1-AS1	ENST00000690912.1 linkuse as main transcript	n.228-17905G>A		intron_variant
EPHA1-AS1	ENST00000703017.1 linkuse as main transcript	n.206-17905G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33214

AN:

151846

Hom.:

4420

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0594

Gnomad AMI

AF:

0.150

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.318

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.232

GnomAD3 exomes

AF:

0.266

AC:

66240

AN:

249162

Hom.:

9242

AF XY:

0.270

AC XY:

36547

AN XY:

135182

show subpopulations

Gnomad AFR exome

AF:

0.0555

Gnomad AMR exome

AF:

0.290

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.274

Gnomad SAS exome

AF:

0.320

Gnomad FIN exome

AF:

0.272

Gnomad NFE exome

AF:

0.272

Gnomad OTH exome

AF:

0.259

GnomAD4 exome

AF:

0.275

AC:

401645

AN:

1461880

Hom.:

56345

Cov.:

AF XY:

0.277

AC XY:

201104

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.0504

Gnomad4 AMR exome

AF:

0.289

Gnomad4 ASJ exome

AF:

0.253

Gnomad4 EAS exome

AF:

0.315

Gnomad4 SAS exome

AF:

0.316

Gnomad4 FIN exome

AF:

0.269

Gnomad4 NFE exome

AF:

0.278

Gnomad4 OTH exome

AF:

0.265

GnomAD4 genome

AF:

0.219

AC:

33232

AN:

151964

Hom.:

4429

Cov.:

AF XY:

0.223

AC XY:

16531

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.0593

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.260

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.321

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.231

Alfa

AF:

0.254

Hom.:

6633

Bravo

AF:

0.209

Asia WGS

AF:

0.271

AC:

944

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

4.3

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over