dbSNP rs9389004: TAAR9:p.Ala278Thr (chr6-132539121-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_175057.4(TAAR9):c.832G>A(p.Ala278Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 1,563,556 control chromosomes in the GnomAD database, including 1,818 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 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 0.037 ( 160 hom., cov: 32)

Exomes 𝑓: 0.046 ( 1658 hom. )

Consequence

TAAR9
NM_175057.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.509

Publications

8 publications found

Variant links:

Genes affected

TAAR9 (HGNC:20977): (trace amine associated receptor 9) TAAR9 is a member of a large family of rhodopsin G protein-coupled receptors (GPCRs, or GPRs). GPCRs contain 7 transmembrane domains and transduce extracellular signals through heterotrimeric G proteins.[supplied by OMIM, Jul 2005]

TAAR9 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=0.0019289851).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0372 (5658/152276) while in subpopulation NFE AF = 0.0514 (3494/68010). AF 95% confidence interval is 0.05. There are 160 homozygotes in GnomAd4. There are 2839 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 160 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAAR9	NM_175057.4 link	c.832G>A	p.Ala278Thr	missense_variant	Exon 1 of 1	ENST00000434551.3	NP_778227.3	Q96RI9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAAR9	ENST00000434551.3 link	c.832G>A	p.Ala278Thr	missense_variant	Exon 1 of 1	6	NM_175057.4	ENSP00000424607.2		Q96RI9

Frequencies

GnomAD3 genomes

AF:

0.0372

AC:

5654

AN:

152158

Hom.:

160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00789

Gnomad AMI

AF:

0.134

Gnomad AMR

AF:

0.0259

Gnomad ASJ

AF:

0.0141

Gnomad EAS

AF:

0.0104

Gnomad SAS

AF:

0.0317

Gnomad FIN

AF:

0.0927

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0514

Gnomad OTH

AF:

0.0311

GnomAD2 exomes

AF:

0.0403

AC:

7860

AN:

195240

AF XY:

0.0413

show subpopulations

Gnomad AFR exome

AF:

0.00896

Gnomad AMR exome

AF:

0.0174

Gnomad ASJ exome

AF:

0.0162

Gnomad EAS exome

AF:

0.00766

Gnomad FIN exome

AF:

0.0914

Gnomad NFE exome

AF:

0.0490

Gnomad OTH exome

AF:

0.0462

GnomAD4 exome

AF:

0.0457

AC:

64533

AN:

1411280

Hom.:

1658

Cov.:

AF XY:

0.0457

AC XY:

31909

AN XY:

698614

show subpopulations

African (AFR)

AF:

0.00736

AC:

231

AN:

31384

American (AMR)

AF:

0.0183

AC:

630

AN:

34388

Ashkenazi Jewish (ASJ)

AF:

0.0160

AC:

370

AN:

23196

East Asian (EAS)

AF:

0.0101

AC:

395

AN:

39282

South Asian (SAS)

AF:

0.0343

AC:

2638

AN:

76980

European-Finnish (FIN)

AF:

0.0937

AC:

4807

AN:

51296

Middle Eastern (MID)

AF:

0.0412

AC:

228

AN:

5534

European-Non Finnish (NFE)

AF:

0.0484

AC:

52818

AN:

1090912

Other (OTH)

AF:

0.0414

AC:

2416

AN:

58308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

3372

6744

10117

13489

16861

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1894

3788

5682

7576

9470

<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:

0.0372

AC:

5658

AN:

152276

Hom.:

160

Cov.:

AF XY:

0.0381

AC XY:

2839

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.00787

AC:

327

AN:

41556

American (AMR)

AF:

0.0260

AC:

398

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0141

AC:

AN:

3470

East Asian (EAS)

AF:

0.0104

AC:

AN:

5186

South Asian (SAS)

AF:

0.0315

AC:

152

AN:

4822

European-Finnish (FIN)

AF:

0.0927

AC:

984

AN:

10616

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0514

AC:

3494

AN:

68010

Other (OTH)

AF:

0.0336

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

278

555

833

1110

1388

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

186

248

310

<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:

0.0425

Hom.:

481

Bravo

AF:

0.0303

TwinsUK

AF:

0.0520

AC:

193

ALSPAC

AF:

0.0485

AC:

187

ESP6500AA

AF:

0.00958

AC:

ESP6500EA

AF:

0.0488

AC:

401

ExAC

AF:

0.0378

AC:

4561

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.19

CADD

Benign

(source)

DANN

Benign

0.37

DEOGEN2

Benign

0.013

FATHMM_MKL

Benign

0.054

LIST_S2

Benign

0.61

MetaRNN

Benign

0.0019

MutationAssessor

Benign

-0.56

PhyloP100

0.51

PrimateAI

Benign

0.29

Sift4G

Benign

1.0

Polyphen

0.0030

Vest4

0.031

GERP RS

1.3

Varity_R

0.099

gMVP

0.065

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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