Genetic Variant NM_003967.3:c.192G>A (chr6-132589495-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_003967.3(TAAR5):c.192G>A(p.Ala64Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 1,613,708 control chromosomes in the GnomAD database, including 15,948 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 0.14 ( 1941 hom., cov: 28)

Exomes 𝑓: 0.12 ( 14007 hom. )

Consequence

TAAR5
NM_003967.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.01

Publications

14 publications found

Variant links:

Genes affected

TAAR5 (HGNC:30236): (trace amine associated receptor 5) Enables trimethylamine receptor activity. Predicted to be involved in signal transduction. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TAAR5 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=-0.6).

BP7

Synonymous conserved (PhyloP=-3.01 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR5	NM_003967.3 link	c.192G>A	p.Ala64Ala	synonymous_variant	Exon 1 of 1	ENST00000258034.4	NP_003958.2	O14804
TAAR5	NM_001389527.1 link	c.192G>A	p.Ala64Ala	synonymous_variant	Exon 4 of 4		NP_001376456.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR5	ENST00000258034.4 link	c.192G>A	p.Ala64Ala	synonymous_variant	Exon 1 of 1	6	NM_003967.3	ENSP00000258034.2		O14804

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21606

AN:

151888

Hom.:

1940

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.157

Gnomad AMR

AF:

0.203

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.326

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.0704

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.0917

Gnomad OTH

AF:

0.170

GnomAD2 exomes

AF:

0.161

AC:

40391

AN:

250610

AF XY:

0.165

show subpopulations

Gnomad AFR exome

AF:

0.177

Gnomad AMR exome

AF:

0.214

Gnomad ASJ exome

AF:

0.159

Gnomad EAS exome

AF:

0.309

Gnomad FIN exome

AF:

0.0693

Gnomad NFE exome

AF:

0.0941

Gnomad OTH exome

AF:

0.156

GnomAD4 exome

AF:

0.117

AC:

171393

AN:

1461702

Hom.:

14007

Cov.:

AF XY:

0.123

AC XY:

89225

AN XY:

727146

show subpopulations

African (AFR)

AF:

0.182

AC:

6079

AN:

33478

American (AMR)

AF:

0.212

AC:

9462

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

4085

AN:

26124

East Asian (EAS)

AF:

0.321

AC:

12719

AN:

39684

South Asian (SAS)

AF:

0.315

AC:

27150

AN:

86236

European-Finnish (FIN)

AF:

0.0682

AC:

3643

AN:

53408

Middle Eastern (MID)

AF:

0.205

AC:

1181

AN:

5766

European-Non Finnish (NFE)

AF:

0.0886

AC:

98508

AN:

1111900

Other (OTH)

AF:

0.142

AC:

8566

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

8661

17322

25984

34645

43306

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3958

7916

11874

15832

19790

<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:

0.142

AC:

21625

AN:

152006

Hom.:

1941

Cov.:

AF XY:

0.149

AC XY:

11071

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.174

AC:

7188

AN:

41428

American (AMR)

AF:

0.203

AC:

3092

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.159

AC:

551

AN:

3466

East Asian (EAS)

AF:

0.327

AC:

1686

AN:

5160

South Asian (SAS)

AF:

0.325

AC:

1567

AN:

4818

European-Finnish (FIN)

AF:

0.0704

AC:

745

AN:

10584

Middle Eastern (MID)

AF:

0.207

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0916

AC:

6228

AN:

67964

Other (OTH)

AF:

0.172

AC:

364

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

898

1797

2695

3594

4492

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

248

496

744

992

1240

<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:

0.116

Hom.:

2383

Bravo

AF:

0.149

Asia WGS

AF:

0.323

AC:

1122

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

1.2

(source)

DANN

Benign

0.76

PhyloP100

-3.0

PromoterAI

-0.0068

Neutral

(source)

Mutation Taster

=99/1

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