Genetic Variant TAS2R60:p.Arg310Arg (chr7-143444382-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_177437.1(TAS2R60):c.930T>C(p.Arg310Arg) 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

Publications

34 publications found

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:

ENSG00000309456 (HGNC:):

ENSG00000309456 links:

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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=-0.91).

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_177437.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAS2R60	NM_177437.1	MANE Select	c.930T>C	p.Arg310Arg	synonymous	Exon 1 of 1	NP_803186.1	P59551
	EPHA1-AS1	NR_033897.1		n.206+29183T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TAS2R60	ENST00000332690.1	TSL:6 MANE Select	c.930T>C	p.Arg310Arg	synonymous	Exon 1 of 1	ENSP00000327724.1	P59551
EPHA1-AS1	ENST00000429289.5	TSL:1	n.206+29183T>C		intron	N/A
EPHA1-AS1	ENST00000690912.2		n.227+29183T>C		intron	N/A

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

GnomAD2 exomes

AF:

0.705

AC:

173606

AN:

246260

AF XY:

0.704

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 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

African (AFR)

AF:

0.538

AC:

17975

AN:

33438

American (AMR)

AF:

0.831

AC:

37140

AN:

44676

Ashkenazi Jewish (ASJ)

AF:

0.598

AC:

15605

AN:

26102

East Asian (EAS)

AF:

0.892

AC:

35422

AN:

39696

South Asian (SAS)

AF:

0.749

AC:

64503

AN:

86136

European-Finnish (FIN)

AF:

0.663

AC:

31178

AN:

46996

Middle Eastern (MID)

AF:

0.617

AC:

3356

AN:

5438

European-Non Finnish (NFE)

AF:

0.674

AC:

748842

AN:

1111516

Other (OTH)

AF:

0.680

AC:

41012

AN:

60308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

16072

32144

48217

64289

80361

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19428

38856

58284

77712

97140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.653

AC:

99250

AN:

151948

Hom.:

33087

Cov.:

AF XY:

0.658

AC XY:

48816

AN XY:

74242

show subpopulations

African (AFR)

AF:

0.548

AC:

22700

AN:

41440

American (AMR)

AF:

0.761

AC:

11632

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.603

AC:

2091

AN:

3468

East Asian (EAS)

AF:

0.875

AC:

4517

AN:

5162

South Asian (SAS)

AF:

0.773

AC:

3715

AN:

4808

European-Finnish (FIN)

AF:

0.653

AC:

6880

AN:

10528

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.671

AC:

45570

AN:

67940

Other (OTH)

AF:

0.655

AC:

1380

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1664

3328

4992

6656

8320

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.667

Hom.:

65240

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.76

(source)

DANN

Benign

0.45

PhyloP100

-1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over