dbSNP rs8192619: TAAR1:p.Cys265Cys (chr6-132645209-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

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

The NM_138327.4(TAAR1):c.795C>T(p.Cys265Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0601 in 1,613,326 control chromosomes in the GnomAD database, including 3,271 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 0.062 ( 336 hom., cov: 32)

Exomes 𝑓: 0.060 ( 2935 hom. )

Consequence

TAAR1
NM_138327.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.754

Publications

23 publications found

Variant links:

Genes affected

TAAR1 (HGNC:17734): (trace amine associated receptor 1) The protein encoded by this gene is a G-protein coupled receptor activated by trace amines. The encoded protein responds little or not at all to dopamine, serotonin, epinephrine, or histamine, but responds well to beta-phenylethylamine, p-tyramine, octopamine, and tryptamine. While primarily functioning in neurologic systems, there is evidence that this gene is involved in blood cell and immunologic functions as well. This gene is thought to be intronless. [provided by RefSeq, Nov 2015]

TAAR1 links:

Genome browser will be placed here

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=-0.66).

BP7

Synonymous conserved (PhyloP=-0.754 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR1	NM_138327.4 link	c.795C>T	p.Cys265Cys	synonymous_variant	Exon 2 of 2	ENST00000275216.3	NP_612200.1	Q96RJ0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR1	ENST00000275216.3 link	c.795C>T	p.Cys265Cys	synonymous_variant	Exon 2 of 2	6	NM_138327.4	ENSP00000275216.1		Q96RJ0

Frequencies

GnomAD3 genomes

AF:

0.0621

AC:

9437

AN:

151956

Hom.:

335

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0590

Gnomad AMI

AF:

0.0187

Gnomad AMR

AF:

0.0774

Gnomad ASJ

AF:

0.0219

Gnomad EAS

AF:

0.111

Gnomad SAS

AF:

0.0861

Gnomad FIN

AF:

0.0749

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0561

Gnomad OTH

AF:

0.0531

GnomAD2 exomes

AF:

0.0666

AC:

16703

AN:

250760

AF XY:

0.0666

show subpopulations

Gnomad AFR exome

AF:

0.0605

Gnomad AMR exome

AF:

0.0845

Gnomad ASJ exome

AF:

0.0200

Gnomad EAS exome

AF:

0.110

Gnomad FIN exome

AF:

0.0793

Gnomad NFE exome

AF:

0.0525

Gnomad OTH exome

AF:

0.0557

GnomAD4 exome

AF:

0.0599

AC:

87502

AN:

1461252

Hom.:

2935

Cov.:

AF XY:

0.0605

AC XY:

43966

AN XY:

726922

show subpopulations

African (AFR)

AF:

0.0594

AC:

1985

AN:

33424

American (AMR)

AF:

0.0861

AC:

3843

AN:

44638

Ashkenazi Jewish (ASJ)

AF:

0.0194

AC:

507

AN:

26098

East Asian (EAS)

AF:

0.112

AC:

4442

AN:

39668

South Asian (SAS)

AF:

0.0860

AC:

7418

AN:

86206

European-Finnish (FIN)

AF:

0.0765

AC:

4082

AN:

53386

Middle Eastern (MID)

AF:

0.0423

AC:

244

AN:

5762

European-Non Finnish (NFE)

AF:

0.0551

AC:

61272

AN:

1111708

Other (OTH)

AF:

0.0614

AC:

3709

AN:

60362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

4675

9349

14024

18698

23373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2412

4824

7236

9648

12060

<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:

0.0622

AC:

9455

AN:

152074

Hom.:

336

Cov.:

AF XY:

0.0647

AC XY:

4807

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.0592

AC:

2457

AN:

41494

American (AMR)

AF:

0.0772

AC:

1178

AN:

15252

Ashkenazi Jewish (ASJ)

AF:

0.0219

AC:

AN:

3468

East Asian (EAS)

AF:

0.111

AC:

573

AN:

5172

South Asian (SAS)

AF:

0.0879

AC:

423

AN:

4814

European-Finnish (FIN)

AF:

0.0749

AC:

793

AN:

10594

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0561

AC:

3814

AN:

67964

Other (OTH)

AF:

0.0530

AC:

112

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

450

901

1351

1802

2252

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<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:

0.0540

Hom.:

391

Bravo

AF:

0.0594

Asia WGS

AF:

0.0810

AC:

283

AN:

3476

EpiCase

AF:

0.0518

EpiControl

AF:

0.0526

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

4.1

(source)

DANN

Benign

0.53

PhyloP100

-0.75

Mutation Taster

=90/10

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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