Genetic Variant NM_175067.1:c.793G>A (chr6-132571114-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.793G>A(p.Val265Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.079 in 1,613,938 control chromosomes in the GnomAD database, including 5,547 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 0.076 ( 503 hom., cov: 32)

Exomes 𝑓: 0.079 ( 5044 hom. )

Consequence

TAAR6
NM_175067.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.832

Publications

25 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (MetaRNN=0.0027578175).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR6	NM_175067.1 link	c.793G>A	p.Val265Ile	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.793G>A	p.Val265Ile	missense_variant	Exon 1 of 1	6	NM_175067.1	ENSP00000275198.1

Frequencies

GnomAD3 genomes

AF:

0.0757

AC:

11506

AN:

152060

Hom.:

503

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0605

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.0560

Gnomad ASJ

AF:

0.0418

Gnomad EAS

AF:

0.0139

Gnomad SAS

AF:

0.0742

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0880

Gnomad OTH

AF:

0.0664

GnomAD2 exomes

AF:

0.0730

AC:

18311

AN:

250952

AF XY:

0.0757

show subpopulations

Gnomad AFR exome

AF:

0.0616

Gnomad AMR exome

AF:

0.0373

Gnomad ASJ exome

AF:

0.0465

Gnomad EAS exome

AF:

0.0105

Gnomad FIN exome

AF:

0.114

Gnomad NFE exome

AF:

0.0872

Gnomad OTH exome

AF:

0.0848

GnomAD4 exome

AF:

0.0794

AC:

116034

AN:

1461760

Hom.:

5044

Cov.:

AF XY:

0.0801

AC XY:

58226

AN XY:

727186

show subpopulations

African (AFR)

AF:

0.0600

AC:

2009

AN:

33474

American (AMR)

AF:

0.0397

AC:

1774

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.0432

AC:

1128

AN:

26130

East Asian (EAS)

AF:

0.0147

AC:

584

AN:

39674

South Asian (SAS)

AF:

0.0824

AC:

7107

AN:

86250

European-Finnish (FIN)

AF:

0.116

AC:

6204

AN:

53412

Middle Eastern (MID)

AF:

0.0890

AC:

513

AN:

5766

European-Non Finnish (NFE)

AF:

0.0828

AC:

92124

AN:

1111944

Other (OTH)

AF:

0.0760

AC:

4591

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

6440

12879

19319

25758

32198

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3214

6428

9642

12856

16070

<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:

0.0756

AC:

11507

AN:

152178

Hom.:

503

Cov.:

AF XY:

0.0761

AC XY:

5665

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.0603

AC:

2502

AN:

41516

American (AMR)

AF:

0.0560

AC:

857

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0418

AC:

145

AN:

3472

East Asian (EAS)

AF:

0.0141

AC:

AN:

5180

South Asian (SAS)

AF:

0.0739

AC:

356

AN:

4818

European-Finnish (FIN)

AF:

0.116

AC:

1225

AN:

10592

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0881

AC:

5987

AN:

67990

Other (OTH)

AF:

0.0681

AC:

144

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

542

1084

1627

2169

2711

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<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:

0.0793

Hom.:

2264

Bravo

AF:

0.0701

TwinsUK

AF:

0.0766

AC:

284

ALSPAC

AF:

0.0828

AC:

319

ESP6500AA

AF:

0.0629

AC:

277

ESP6500EA

AF:

0.0807

AC:

694

ExAC

AF:

0.0759

AC:

9219

Asia WGS

AF:

0.0410

AC:

143

AN:

3478

EpiCase

AF:

0.0847

EpiControl

AF:

0.0903

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.094

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.72

CADD

Benign

0.024

(source)

DANN

Benign

0.61

DEOGEN2

Benign

0.010

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.090

LIST_S2

Benign

0.44

MetaRNN

Benign

0.0028

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.37

PhyloP100

-0.83

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.60

REVEL

Benign

0.028

Sift

Benign

0.83

Sift4G

Benign

0.94

Polyphen

0.0

Vest4

0.014

MPC

0.0097

ClinPred

0.0022

GERP RS

-6.0

Varity_R

0.037

gMVP

0.018

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