dbSNP rs1404635: TAS2R41:p.Thr63Thr (chr7-143478061-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

25 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TAS2R41	NM_176883.2 link	c.189G>A	p.Thr63Thr	synonymous_variant	Exon 1 of 1	ENST00000408916.1	NP_795364.2	P59536
EPHA1-AS1	NR_033897.1 link	n.207-26713G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R41	ENST00000408916.1 link	c.189G>A	p.Thr63Thr	synonymous_variant	Exon 1 of 1	6	NM_176883.2	ENSP00000386201.1		P59536

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

GnomAD2 exomes

AF:

0.266

AC:

66240

AN:

249162

AF XY:

0.270

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 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

African (AFR)

AF:

0.0504

AC:

1688

AN:

33480

American (AMR)

AF:

0.289

AC:

12935

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.253

AC:

6620

AN:

26136

East Asian (EAS)

AF:

0.315

AC:

12497

AN:

39700

South Asian (SAS)

AF:

0.316

AC:

27299

AN:

86258

European-Finnish (FIN)

AF:

0.269

AC:

14366

AN:

53420

Middle Eastern (MID)

AF:

0.200

AC:

1152

AN:

5768

European-Non Finnish (NFE)

AF:

0.278

AC:

309107

AN:

1111998

Other (OTH)

AF:

0.265

AC:

15981

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

19839

39677

59516

79354

99193

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.219

AC:

33232

AN:

151964

Hom.:

4429

Cov.:

AF XY:

0.223

AC XY:

16531

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.0593

AC:

2459

AN:

41490

American (AMR)

AF:

0.282

AC:

4310

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

901

AN:

3466

East Asian (EAS)

AF:

0.291

AC:

1497

AN:

5140

South Asian (SAS)

AF:

0.321

AC:

1543

AN:

4814

European-Finnish (FIN)

AF:

0.266

AC:

2802

AN:

10538

Middle Eastern (MID)

AF:

0.150

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.280

AC:

19052

AN:

67934

Other (OTH)

AF:

0.231

AC:

487

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1247

2494

3741

4988

6235

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.250

Hom.:

8067

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

(source)

DANN

Benign

0.60

PhyloP100

0.14

PromoterAI

-0.0027

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs1404635

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over