Genetic Variant TAAR6:p.Pro26Pro (chr6-132570399-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_175067.1(TAAR6):c.78C>T(p.Pro26Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 1,614,040 control chromosomes in the GnomAD database, including 2,001 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 0.037 ( 151 hom., cov: 32)

Exomes 𝑓: 0.047 ( 1850 hom. )

Consequence

TAAR6
NM_175067.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

9 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP7

Synonymous conserved (PhyloP=-1.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR6	NM_175067.1 link	c.78C>T	p.Pro26Pro	synonymous_variant	Exon 1 of 1	ENST00000275198.1	NP_778237.1	Q96RI8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR6	ENST00000275198.1 link	c.78C>T	p.Pro26Pro	synonymous_variant	Exon 1 of 1	6	NM_175067.1	ENSP00000275198.1		Q96RI8

Frequencies

GnomAD3 genomes

AF:

0.0369

AC:

5612

AN:

152122

Hom.:

151

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00869

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.0225

Gnomad ASJ

AF:

0.0181

Gnomad EAS

AF:

0.00847

Gnomad SAS

AF:

0.0323

Gnomad FIN

AF:

0.0627

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0556

Gnomad OTH

AF:

0.0320

GnomAD2 exomes

AF:

0.0394

AC:

9880

AN:

250990

AF XY:

0.0410

show subpopulations

Gnomad AFR exome

AF:

0.00911

Gnomad AMR exome

AF:

0.0166

Gnomad ASJ exome

AF:

0.0178

Gnomad EAS exome

AF:

0.00572

Gnomad FIN exome

AF:

0.0623

Gnomad NFE exome

AF:

0.0544

Gnomad OTH exome

AF:

0.0454

GnomAD4 exome

AF:

0.0474

AC:

69329

AN:

1461800

Hom.:

1850

Cov.:

AF XY:

0.0474

AC XY:

34491

AN XY:

727200

show subpopulations

African (AFR)

AF:

0.00809

AC:

271

AN:

33478

American (AMR)

AF:

0.0175

AC:

781

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0173

AC:

452

AN:

26130

East Asian (EAS)

AF:

0.00925

AC:

367

AN:

39688

South Asian (SAS)

AF:

0.0341

AC:

2939

AN:

86258

European-Finnish (FIN)

AF:

0.0651

AC:

3476

AN:

53410

Middle Eastern (MID)

AF:

0.0425

AC:

245

AN:

5762

European-Non Finnish (NFE)

AF:

0.0524

AC:

58249

AN:

1111958

Other (OTH)

AF:

0.0422

AC:

2549

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

4167

8334

12502

16669

20836

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2034

4068

6102

8136

10170

<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:

0.0369

AC:

5616

AN:

152240

Hom.:

151

Cov.:

AF XY:

0.0363

AC XY:

2699

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.00866

AC:

360

AN:

41552

American (AMR)

AF:

0.0226

AC:

345

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0181

AC:

AN:

3472

East Asian (EAS)

AF:

0.00849

AC:

AN:

5184

South Asian (SAS)

AF:

0.0324

AC:

156

AN:

4822

European-Finnish (FIN)

AF:

0.0627

AC:

664

AN:

10590

Middle Eastern (MID)

AF:

0.0306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0556

AC:

3779

AN:

68008

Other (OTH)

AF:

0.0340

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

285

571

856

1142

1427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

198

264

330

<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:

0.0421

Hom.:

164

Bravo

AF:

0.0321

Asia WGS

AF:

0.0200

AC:

AN:

3476

EpiCase

AF:

0.0497

EpiControl

AF:

0.0523

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

4.6

(source)

DANN

Benign

0.51

PhyloP100

-1.1

PromoterAI

0.012

Neutral

(source)

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