Variant 7-141790438-G-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_018980.3(TAS2R5):c.77G>T(p.Ser26Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 1,613,890 control chromosomes in the GnomAD database, including 190,670 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 0.43 ( 15162 hom., cov: 32)

Exomes 𝑓: 0.49 ( 175508 hom. )

Consequence

TAS2R5
NM_018980.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.383

Variant links:

Genes affected

TAS2R5 (HGNC:14912): (taste 2 receptor member 5) This gene encodes a bitter taste receptor; bitter taste receptors are members of the G protein-coupled receptor superfamily and are specifically expressed by taste receptor cells of the tongue and palate epithelia. Each of these apparently intronless taste receptor genes encodes a 7-transmembrane receptor protein, functioning as a bitter taste receptor. This gene is clustered with another 3 candidate taste receptor genes on chromosome 7 and is genetically linked to loci that influence bitter perception. [provided by RefSeq, Jul 2008]

TAS2R5 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=2.5815077E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R5	NM_018980.3 linkuse as main transcript	c.77G>T	p.Ser26Ile	missense_variant	1/1	ENST00000247883.5	NP_061853.1	Q9NYW4A4D1U0Q502V5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAS2R5	ENST00000247883.5 linkuse as main transcript	c.77G>T	p.Ser26Ile	missense_variant	1/1	6	NM_018980.3	ENSP00000247883.4		Q9NYW4

Frequencies

GnomAD3 genomes

AF:

0.434

AC:

65879

AN:

151932

Hom.:

15153

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.515

Gnomad ASJ

AF:

0.468

Gnomad EAS

AF:

0.715

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.462

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.456

GnomAD3 exomes

AF:

0.489

AC:

122895

AN:

251354

Hom.:

31303

AF XY:

0.490

AC XY:

66634

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.254

Gnomad AMR exome

AF:

0.532

Gnomad ASJ exome

AF:

0.461

Gnomad EAS exome

AF:

0.720

Gnomad SAS exome

AF:

0.451

Gnomad FIN exome

AF:

0.461

Gnomad NFE exome

AF:

0.490

Gnomad OTH exome

AF:

0.502

GnomAD4 exome

AF:

0.487

AC:

711860

AN:

1461838

Hom.:

175508

Cov.:

AF XY:

0.488

AC XY:

354638

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.253

Gnomad4 AMR exome

AF:

0.535

Gnomad4 ASJ exome

AF:

0.458

Gnomad4 EAS exome

AF:

0.715

Gnomad4 SAS exome

AF:

0.454

Gnomad4 FIN exome

AF:

0.462

Gnomad4 NFE exome

AF:

0.488

Gnomad4 OTH exome

AF:

0.490

GnomAD4 genome

AF:

0.434

AC:

65926

AN:

152052

Hom.:

15162

Cov.:

AF XY:

0.436

AC XY:

32443

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.264

Gnomad4 AMR

AF:

0.515

Gnomad4 ASJ

AF:

0.468

Gnomad4 EAS

AF:

0.715

Gnomad4 SAS

AF:

0.442

Gnomad4 FIN

AF:

0.462

Gnomad4 NFE

AF:

0.492

Gnomad4 OTH

AF:

0.462

Alfa

AF:

0.488

Hom.:

38081

Bravo

AF:

0.434

TwinsUK

AF:

0.489

AC:

1813

ALSPAC

AF:

0.478

AC:

1841

ESP6500AA

AF:

0.255

AC:

1124

ESP6500EA

AF:

0.493

AC:

4239

ExAC

AF:

0.481

AC:

58437

Asia WGS

AF:

0.560

AC:

1947

AN:

3478

EpiCase

AF:

0.500

EpiControl

AF:

0.498

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

1.0

DANN

Benign

0.77

DEOGEN2

Benign

0.0010

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.00016

LIST_S2

Benign

0.18

MetaRNN

Benign

0.0000026

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.34

PrimateAI

Benign

0.24

PROVEAN

Benign

2.2

REVEL

Benign

0.035

Sift

Benign

0.11

Sift4G

Benign

0.80

Polyphen

0.0

Vest4

0.040

MPC

0.082

ClinPred

0.0059

GERP RS

3.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.070

gMVP

0.073

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

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