Genetic Variant TAAR6:p.Cys291Tyr (chr6-132571193-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_175067.1(TAAR6):c.872G>A(p.Cys291Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0693 in 1,613,852 control chromosomes in the GnomAD database, including 4,185 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 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 0.077 ( 467 hom., cov: 32)

Exomes 𝑓: 0.069 ( 3718 hom. )

Consequence

TAAR6
NM_175067.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.554

Publications

22 publications found

Variant links:

Genes affected

TAAR6 (HGNC:20978): (trace amine associated receptor 6) This gene encodes a seven-transmembrane G-protein-coupled receptor that likely functions as a receptor for endogenous trace amines. Mutations in this gene may be associated with schizophrenia.[provided by RefSeq, Feb 2010]

TAAR6 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=0.0021861494).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR6	NM_175067.1 link	c.872G>A	p.Cys291Tyr	missense_variant	Exon 1 of 1	ENST00000275198.1	NP_778237.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR6	ENST00000275198.1 link	c.872G>A	p.Cys291Tyr	missense_variant	Exon 1 of 1	6	NM_175067.1	ENSP00000275198.1

Frequencies

GnomAD3 genomes

AF:

0.0766

AC:

11636

AN:

151984

Hom.:

467

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.0476

Gnomad ASJ

AF:

0.0280

Gnomad EAS

AF:

0.0127

Gnomad SAS

AF:

0.0631

Gnomad FIN

AF:

0.0802

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0740

Gnomad OTH

AF:

0.0657

GnomAD2 exomes

AF:

0.0619

AC:

15536

AN:

250970

AF XY:

0.0629

show subpopulations

Gnomad AFR exome

AF:

0.104

Gnomad AMR exome

AF:

0.0292

Gnomad ASJ exome

AF:

0.0278

Gnomad EAS exome

AF:

0.00925

Gnomad FIN exome

AF:

0.0790

Gnomad NFE exome

AF:

0.0718

Gnomad OTH exome

AF:

0.0652

GnomAD4 exome

AF:

0.0686

AC:

100204

AN:

1461750

Hom.:

3718

Cov.:

AF XY:

0.0685

AC XY:

49791

AN XY:

727186

show subpopulations

African (AFR)

AF:

0.108

AC:

3625

AN:

33474

American (AMR)

AF:

0.0305

AC:

1362

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.0246

AC:

642

AN:

26134

East Asian (EAS)

AF:

0.0137

AC:

542

AN:

39694

South Asian (SAS)

AF:

0.0693

AC:

5978

AN:

86252

European-Finnish (FIN)

AF:

0.0817

AC:

4363

AN:

53418

Middle Eastern (MID)

AF:

0.0637

AC:

367

AN:

5764

European-Non Finnish (NFE)

AF:

0.0714

AC:

79402

AN:

1111900

Other (OTH)

AF:

0.0650

AC:

3923

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

5532

11064

16595

22127

27659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2862

5724

8586

11448

14310

<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:

0.0766

AC:

11645

AN:

152102

Hom.:

467

Cov.:

AF XY:

0.0754

AC XY:

5607

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.103

AC:

4260

AN:

41478

American (AMR)

AF:

0.0476

AC:

728

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0280

AC:

AN:

3468

East Asian (EAS)

AF:

0.0129

AC:

AN:

5176

South Asian (SAS)

AF:

0.0623

AC:

300

AN:

4812

European-Finnish (FIN)

AF:

0.0802

AC:

848

AN:

10576

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0740

AC:

5033

AN:

67996

Other (OTH)

AF:

0.0674

AC:

142

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

553

1107

1660

2214

2767

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

130

260

390

520

650

<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:

0.0718

Hom.:

1621

Bravo

AF:

0.0730

TwinsUK

AF:

0.0701

AC:

260

ALSPAC

AF:

0.0737

AC:

284

ESP6500AA

AF:

0.103

AC:

456

ESP6500EA

AF:

0.0677

AC:

582

ExAC

AF:

0.0645

AC:

7831

Asia WGS

AF:

0.0510

AC:

175

AN:

3478

EpiCase

AF:

0.0677

EpiControl

AF:

0.0677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.080

BayesDel_addAF

Benign

-0.72

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.53

(source)

DANN

Benign

0.18

DEOGEN2

Benign

0.0072

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.012

LIST_S2

Benign

0.53

MetaRNN

Benign

0.0022

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-1.9

PhyloP100

0.55

PrimateAI

Benign

0.35

PROVEAN

Benign

3.3

REVEL

Benign

0.13

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.020

MPC

0.0088

ClinPred

0.0021

GERP RS

3.9

Varity_R

0.049

gMVP

0.12

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over