Genetic Variant NM_181429.2:c.794G>A (chr12-11186144-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_181429.2(TAS2R42):c.794G>A(p.Cys265Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 1,613,684 control chromosomes in the GnomAD database, including 461,752 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/5 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.76 ( 44199 hom., cov: 32)

Exomes 𝑓: 0.76 ( 417553 hom. )

Consequence

TAS2R42
NM_181429.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.26

Publications

31 publications found

Variant links:

Genes affected

TAS2R42 (HGNC:18888): (taste 2 receptor member 42) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway and sensory perception of taste. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TAS2R42 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0069088936).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS2R42	NM_181429.2 link	c.794G>A	p.Cys265Tyr	missense_variant	Exon 1 of 1	ENST00000334266.1	NP_852094.2	Q7RTR8A0A0G2JPZ2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS2R42	ENST00000334266.1 link	c.794G>A	p.Cys265Tyr	missense_variant	Exon 1 of 1	6	NM_181429.2	ENSP00000334050.1		Q7RTR8

Frequencies

GnomAD3 genomes

AF:

0.762

AC:

115825

AN:

152008

Hom.:

44153

Cov.:

show subpopulations

Gnomad AFR

AF:

0.766

Gnomad AMI

AF:

0.848

Gnomad AMR

AF:

0.771

Gnomad ASJ

AF:

0.809

Gnomad EAS

AF:

0.782

Gnomad SAS

AF:

0.784

Gnomad FIN

AF:

0.742

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.753

Gnomad OTH

AF:

0.773

GnomAD4 exome

AF:

0.755

AC:

1104134

AN:

1461558

Hom.:

417553

Cov.:

AF XY:

0.756

AC XY:

550009

AN XY:

727084

show subpopulations

African (AFR)

AF:

0.759

AC:

25419

AN:

33470

American (AMR)

AF:

0.753

AC:

33642

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.808

AC:

21115

AN:

26134

East Asian (EAS)

AF:

0.777

AC:

30847

AN:

39692

South Asian (SAS)

AF:

0.787

AC:

67910

AN:

86246

European-Finnish (FIN)

AF:

0.745

AC:

39768

AN:

53404

Middle Eastern (MID)

AF:

0.801

AC:

4617

AN:

5764

European-Non Finnish (NFE)

AF:

0.751

AC:

834854

AN:

1111768

Other (OTH)

AF:

0.761

AC:

45962

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.541

Heterozygous variant carriers

14843

29686

44528

59371

74214

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20342

40684

61026

81368

101710

<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:

0.762

AC:

115924

AN:

152126

Hom.:

44199

Cov.:

AF XY:

0.760

AC XY:

56558

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.766

AC:

31804

AN:

41498

American (AMR)

AF:

0.771

AC:

11780

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.809

AC:

2808

AN:

3470

East Asian (EAS)

AF:

0.782

AC:

4046

AN:

5172

South Asian (SAS)

AF:

0.784

AC:

3779

AN:

4818

European-Finnish (FIN)

AF:

0.742

AC:

7845

AN:

10570

Middle Eastern (MID)

AF:

0.786

AC:

231

AN:

294

European-Non Finnish (NFE)

AF:

0.753

AC:

51222

AN:

68000

Other (OTH)

AF:

0.775

AC:

1636

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1462

2923

4385

5846

7308

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

860

1720

2580

3440

4300

<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:

0.762

Hom.:

141954

Bravo

AF:

0.765

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.062

CADD

Benign

0.0030

(source)

MetaRNN

Benign

0.0069

PhyloP100

-1.3

Sift4G

Benign

1.0

Vest4

0.037

gMVP

0.14

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over