Variant 7-143444382-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_177437.1(TAS2R60):c.930T>C(p.Arg310=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 1,606,254 control chromosomes in the GnomAD database, including 376,327 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 0.65 ( 33087 hom., cov: 30)

Exomes 𝑓: 0.68 ( 343240 hom. )

Consequence

TAS2R60
NM_177437.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.58

Variant links:

Genes affected

TAS2R60 (HGNC:20639): (taste 2 receptor member 60) 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. [provided by RefSeq, Jul 2017]

TAS2R60 links:

EPHA1-AS1 (HGNC:27799): (EPHA1 antisense RNA 1)

EPHA1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP7

Synonymous conserved (PhyloP=-1.58 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAS2R60	NM_177437.1 linkuse as main transcript	c.930T>C	p.Arg310=	synonymous_variant	1/1	ENST00000332690.1	NP_803186.1
EPHA1-AS1	NR_033897.1 linkuse as main transcript	n.206+29183T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
TAS2R60	ENST00000332690.1 linkuse as main transcript	c.930T>C	p.Arg310=	synonymous_variant	1/1		NM_177437.1	ENSP00000327724	P1
EPHA1-AS1	ENST00000429289.5 linkuse as main transcript	n.206+29183T>C		intron_variant, non_coding_transcript_variant		1
EPHA1-AS1	ENST00000690912.1 linkuse as main transcript	n.227+29183T>C		intron_variant, non_coding_transcript_variant
EPHA1-AS1	ENST00000703017.1 linkuse as main transcript	n.205+29183T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.653

AC:

99176

AN:

151830

Hom.:

33062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.548

Gnomad AMI

AF:

0.636

Gnomad AMR

AF:

0.760

Gnomad ASJ

AF:

0.603

Gnomad EAS

AF:

0.876

Gnomad SAS

AF:

0.772

Gnomad FIN

AF:

0.653

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.671

Gnomad OTH

AF:

0.655

GnomAD3 exomes

AF:

0.705

AC:

173606

AN:

246260

Hom.:

62505

AF XY:

0.704

AC XY:

93983

AN XY:

133464

show subpopulations

Gnomad AFR exome

AF:

0.543

Gnomad AMR exome

AF:

0.841

Gnomad ASJ exome

AF:

0.599

Gnomad EAS exome

AF:

0.870

Gnomad SAS exome

AF:

0.751

Gnomad FIN exome

AF:

0.655

Gnomad NFE exome

AF:

0.665

Gnomad OTH exome

AF:

0.693

GnomAD4 exome

AF:

0.684

AC:

995033

AN:

1454306

Hom.:

343240

Cov.:

AF XY:

0.686

AC XY:

496250

AN XY:

723660

show subpopulations

Gnomad4 AFR exome

AF:

0.538

Gnomad4 AMR exome

AF:

0.831

Gnomad4 ASJ exome

AF:

0.598

Gnomad4 EAS exome

AF:

0.892

Gnomad4 SAS exome

AF:

0.749

Gnomad4 FIN exome

AF:

0.663

Gnomad4 NFE exome

AF:

0.674

Gnomad4 OTH exome

AF:

0.680

GnomAD4 genome

AF:

0.653

AC:

99250

AN:

151948

Hom.:

33087

Cov.:

AF XY:

0.658

AC XY:

48816

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.548

Gnomad4 AMR

AF:

0.761

Gnomad4 ASJ

AF:

0.603

Gnomad4 EAS

AF:

0.875

Gnomad4 SAS

AF:

0.773

Gnomad4 FIN

AF:

0.653

Gnomad4 NFE

AF:

0.671

Gnomad4 OTH

AF:

0.655

Alfa

AF:

0.667

Hom.:

48424

Bravo

AF:

0.656

Asia WGS

AF:

0.775

AC:

2693

AN:

3478

EpiCase

AF:

0.661

EpiControl

AF:

0.657

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.76

DANN

Benign

0.45

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