Variant 7-143478252-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_176883.2(TAS2R41):c.380C>T(p.Pro127Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 1,613,772 control chromosomes in the GnomAD database, including 60,758 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.22 ( 4414 hom., cov: 30)

Exomes 𝑓: 0.27 ( 56344 hom. )

Consequence

TAS2R41
NM_176883.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00100

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:27799): (EPHA1 antisense RNA 1)

EPHA1-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004470557).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAS2R41	NM_176883.2 linkuse as main transcript	c.380C>T	p.Pro127Leu	missense_variant	1/1	ENST00000408916.1
EPHA1-AS1	NR_033897.1 linkuse as main transcript	n.207-26522C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
TAS2R41	ENST00000408916.1 linkuse as main transcript	c.380C>T	p.Pro127Leu	missense_variant	1/1		NM_176883.2	P1
EPHA1-AS1	ENST00000429289.5 linkuse as main transcript	n.207-26522C>T		intron_variant, non_coding_transcript_variant		1
EPHA1-AS1	ENST00000690912.1 linkuse as main transcript	n.228-17714C>T		intron_variant, non_coding_transcript_variant
EPHA1-AS1	ENST00000703017.1 linkuse as main transcript	n.206-17714C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33213

AN:

151858

Hom.:

4405

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0593

Gnomad AMI

AF:

0.151

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.290

Gnomad SAS

AF:

0.319

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:

66216

AN:

249162

Hom.:

9225

AF XY:

0.270

AC XY:

36545

AN XY:

135172

show subpopulations

Gnomad AFR exome

AF:

0.0557

Gnomad AMR exome

AF:

0.289

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.274

Gnomad SAS exome

AF:

0.319

Gnomad FIN exome

AF:

0.272

Gnomad NFE exome

AF:

0.272

Gnomad OTH exome

AF:

0.260

GnomAD4 exome

AF:

0.275

AC:

401655

AN:

1461796

Hom.:

56344

Cov.:

AF XY:

0.277

AC XY:

201114

AN XY:

727204

show subpopulations

Gnomad4 AFR exome

AF:

0.0509

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:

33237

AN:

151976

Hom.:

4414

Cov.:

AF XY:

0.222

AC XY:

16520

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.0594

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.260

Gnomad4 EAS

AF:

0.290

Gnomad4 SAS

AF:

0.321

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.231

Alfa

AF:

0.268

Hom.:

11670

Bravo

AF:

0.209

TwinsUK

AF:

0.261

AC:

967

ALSPAC

AF:

0.279

AC:

1076

ESP6500AA

AF:

0.0595

AC:

232

ESP6500EA

AF:

0.273

AC:

2266

ExAC

AF:

0.262

AC:

31650

Asia WGS

AF:

0.273

AC:

951

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0090

Eigen

Benign

-0.47

Eigen_PC

Benign

-0.47

FATHMM_MKL

Benign

0.039

MetaRNN

Benign

0.0045

MetaSVM

Benign

-0.95

MutationAssessor

Benign

1.9

MutationTaster

Benign

1.0

PrimateAI

Benign

0.31

PROVEAN

Uncertain

-3.8

REVEL

Benign

0.087

Sift

Benign

0.066

Sift4G

Benign

0.085

Polyphen

0.42

Vest4

0.11

MPC

0.12

ClinPred

0.025

GERP RS

1.5

Varity_R

0.11

gMVP

0.15

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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