dbSNP rs8192620: TAAR1:p.Val288Val (chr6-132645140-T-C) – 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.864A>G(p.Val288Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,612,680 control chromosomes in the GnomAD database, including 42,071 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 0.19 ( 3082 hom., cov: 32)

Exomes 𝑓: 0.23 ( 38989 hom. )

Consequence

TAAR1
NM_138327.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.886

Publications

20 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=-0.86).

BP7

Synonymous conserved (PhyloP=-0.886 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR1	NM_138327.4 link	c.864A>G	p.Val288Val	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.864A>G	p.Val288Val	synonymous_variant	Exon 2 of 2	6	NM_138327.4	ENSP00000275216.1		Q96RJ0

Frequencies

GnomAD3 genomes

AF:

0.193

AC:

29321

AN:

151868

Hom.:

3079

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.334

Gnomad SAS

AF:

0.231

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.174

GnomAD2 exomes

AF:

0.220

AC:

54971

AN:

250130

AF XY:

0.223

show subpopulations

Gnomad AFR exome

AF:

0.126

Gnomad AMR exome

AF:

0.165

Gnomad ASJ exome

AF:

0.158

Gnomad EAS exome

AF:

0.340

Gnomad FIN exome

AF:

0.218

Gnomad NFE exome

AF:

0.233

Gnomad OTH exome

AF:

0.214

GnomAD4 exome

AF:

0.228

AC:

332775

AN:

1460694

Hom.:

38989

Cov.:

AF XY:

0.228

AC XY:

165411

AN XY:

726606

show subpopulations

African (AFR)

AF:

0.124

AC:

4156

AN:

33422

American (AMR)

AF:

0.164

AC:

7304

AN:

44580

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

4106

AN:

26078

East Asian (EAS)

AF:

0.344

AC:

13620

AN:

39650

South Asian (SAS)

AF:

0.228

AC:

19582

AN:

86036

European-Finnish (FIN)

AF:

0.222

AC:

11843

AN:

53404

Middle Eastern (MID)

AF:

0.170

AC:

979

AN:

5756

European-Non Finnish (NFE)

AF:

0.232

AC:

257910

AN:

1111426

Other (OTH)

AF:

0.220

AC:

13275

AN:

60342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

14097

28195

42292

56390

70487

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8792

17584

26376

35168

43960

<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:

0.193

AC:

29336

AN:

151986

Hom.:

3082

Cov.:

AF XY:

0.194

AC XY:

14426

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.125

AC:

5182

AN:

41474

American (AMR)

AF:

0.161

AC:

2452

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.161

AC:

556

AN:

3464

East Asian (EAS)

AF:

0.333

AC:

1721

AN:

5166

South Asian (SAS)

AF:

0.229

AC:

1105

AN:

4822

European-Finnish (FIN)

AF:

0.219

AC:

2312

AN:

10576

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.227

AC:

15389

AN:

67916

Other (OTH)

AF:

0.180

AC:

379

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1194

2388

3582

4776

5970

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.209

Hom.:

4223

Bravo

AF:

0.187

Asia WGS

AF:

0.282

AC:

978

AN:

3478

EpiCase

AF:

0.232

EpiControl

AF:

0.221

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.47

(source)

DANN

Benign

0.55

PhyloP100

-0.89

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